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Merge pull request #1148 from martenson/migrate-in-no-2
migrate in samtools, kraken, vcflib
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‎.travis.yml

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@@ -7,6 +7,8 @@ python: 2.7
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env:
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- CHUNK=0
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- CHUNK=1
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- CHUNK=2
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- CHUNK=3
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before_install:
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- export GALAXY_REPO=https://github.com/galaxyproject/galaxy
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planemo ci_find_repos --exclude_from .tt_blacklist \
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--exclude packages --exclude data_managers \
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--changed_in_commit_range "$TRAVIS_COMMIT_RANGE" \
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--chunk_count 2 --chunk "${CHUNK}" \
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--chunk_count 4 --chunk "${CHUNK}" \
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--output changed_repositories_chunk.list
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- cat changed_repositories_chunk.list
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‎tool_collections/kraken/README.rst

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Introduction
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============
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`Kraken <http://ccb.jhu.edu/software/kraken/>`__ is a taxonomic sequence
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classifier that assigns taxonomic labels to short DNA reads. It does
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this by examining the :math:`k`-mers within a read and querying a
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database with those :math:`k`-mers. This database contains a mapping of
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every :math:`k`-mer in
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`Kraken <http://ccb.jhu.edu/software/kraken/>`__'s genomic library to
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the lowest common ancestor (LCA) in a taxonomic tree of all genomes that
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contain that :math:`k`-mer. The set of LCA taxa that correspond to the
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:math:`k`-mers in a read are then analyzed to create a single taxonomic
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label for the read; this label can be any of the nodes in the taxonomic
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tree. `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is designed to be
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rapid, sensitive, and highly precise. Our tests on various real and
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simulated data have shown
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`Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity
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slightly lower than Megablast with precision being slightly higher. On a
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set of simulated 100 bp reads,
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`Kraken <http://ccb.jhu.edu/software/kraken/>`__ processed over 1.3
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million reads per minute on a single core in normal operation, and over
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4.1 million reads per minute in quick operation.
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The latest released version of Kraken will be available at the `Kraken
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website <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates
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to the Kraken source code are available at the `Kraken GitHub
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repository <https://github.com/DerrickWood/kraken>`__.
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If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your
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research, please cite the `Kraken
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paper <http://genomebiology.com/2014/15/3/R46>`__. Thank you!
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System Requirements
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===================
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Note: Users concerned about the disk or memory requirements should read
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the paragraph about MiniKraken, below.
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- **Disk space**: Construction of Kraken's standard database will
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require at least 160 GB of disk space. Customized databases may
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require more or less space. Disk space used is linearly proportional
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to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's
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default database contains just under 6 billion (6e9) distinct
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:math:`k`-mers.
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In addition, the disk used to store the database should be
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locally-attached storage. Storing the database on a network
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filesystem (NFS) partition can cause Kraken's operation to be very
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slow, or to be stopped completely. As NFS accesses are much slower
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than local disk accesses, both preloading and database building will
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be slowed by use of NFS.
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- **Memory**: To run efficiently, Kraken requires enough free memory to
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hold the database in RAM. While this can be accomplished using a
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ramdisk, Kraken supplies a utility for loading the database into RAM
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via the OS cache. The default database size is 75 GB (as of Feb.
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2015), and so you will need at least that much RAM if you want to
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build or run with the default database.
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- **Dependencies**: Kraken currently makes extensive use of Linux
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utilities such as sed, find, and wget. Many scripts are written using
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the Bash shell, and the main scripts are written using Perl. Core
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programs needed to build the database and run the classifier are
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written in C++, and need to be compiled using g++. Multithreading is
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handled using OpenMP. Downloads of NCBI data are performed by wget
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and in some cases, by rsync. Most Linux systems that have any sort of
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development package installed will have all of the above listed
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programs and libraries available.
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Finally, if you want to build your own database, you will need to
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install the
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`Jellyfish <http://www.cbcb.umd.edu/software/jellyfish/>`__
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:math:`k`-mer counter. Note that Kraken only supports use of
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Jellyfish version 1. Jellyfish version 2 is not yet compatible with
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Kraken.
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- **Network connectivity**: Kraken's standard database build and
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download commands expect unfettered FTP and rsync access to the NCBI
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FTP server. If you're working behind a proxy, you may need to set
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certain environment variables (such as ``ftp_proxy`` or
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``RSYNC_PROXY``) in order to get these commands to work properly.
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- **MiniKraken**: To allow users with low-memory computing environments
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to use Kraken, we supply a reduced standard database that can be
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downloaded from the Kraken web site. When Kraken is run with a
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reduced database, we call it MiniKraken.
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The database we make available is only 4 GB in size, and should run
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well on computers with as little as 8 GB of RAM. Disk space required
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for this database is also only 4 GB.
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‎tool_collections/kraken/database.idx

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‎tool_collections/kraken/database.kdb

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‎tool_collections/kraken/kraken/.shed.yml

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categories:
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- Metagenomics
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description: Kraken for taxonomic designation.
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homepage_url: http://ccb.jhu.edu/software/kraken/
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long_description: |
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Kraken is a system for assigning taxonomic labels to short DNA
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sequences, usually obtained through metagenomic studies. Previous attempts by other
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bioinformatics software to accomplish this task have often used sequence alignment
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or machine learning techniques that were quite slow, leading to the development
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of less sensitive but much faster abundance estimation programs. Kraken aims to
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achieve high sensitivity and high speed by utilizing exact alignments of k-mers
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and a novel classification algorithm.
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name: kraken
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owner: devteam
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remote_repository_url: https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/
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type: unrestricted

‎tool_collections/kraken/kraken/README.rst

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../README.rst

‎tool_collections/kraken/kraken/kraken.xml

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<?xml version="1.0"?>
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<tool id="kraken" name="Kraken" version="1.2.1">
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<description>
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assign taxonomic labels to sequencing reads
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</description>
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<macros>
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<import>macros.xml</import>
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</macros>
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<expand macro="requirements" />
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<expand macro="version_command" />
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<command detect_errors="exit_code">
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<![CDATA[
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@SET_DATABASE_PATH@ &&
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kraken
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--threads \${GALAXY_SLOTS:-1}
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@INPUT_DATABASE@
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${only_classified_output}
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#if str( $quick_operation.quick ) == "yes":
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--quick
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--min-hits ${quick_operation.min_hits}
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#end if
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#if $single_paired.single_paired_selector == 'yes'
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#if $forward_input.is_of_type( 'fastq' ):
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--fastq-input
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#else:
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--fasta-input
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#end if
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'${single_paired.forward_input}' '${single_paired.reverse_input}'
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${single_paired.check_names}
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#elif $single_paired.single_paired_selector == "collection":
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#if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
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--fastq-input
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#else:
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--fasta-input
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#end if
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"${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"
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${single_paired.check_names}
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#else:
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#if $single_paired.input_sequences.is_of_type('fastq')
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--fastq-input
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#else:
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--fasta-input
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#end if
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'${single_paired.input_sequences}'
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#end if
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#if $split_reads:
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--classified-out "${classified_out}" --unclassified-out "${unclassified_out}"
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#end if
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## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
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> "${output}"
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##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}"
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]]></command>
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<inputs>
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<conditional name="single_paired">
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<param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
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<option value="collection">Collection</option>
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<option value="yes">Paired</option>
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<option selected="True" value="no">Single</option>
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</param>
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<when value="collection">
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<param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
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<param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
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</when>
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<when value="yes">
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<param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
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<param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
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<param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
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</when>
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<when value="no">
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<param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
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</when>
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</conditional>
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<param name="split_reads" type="boolean" label="Output classified and unclassified reads?" help="Sets --unclassified-out and --classified-out"/>
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<conditional name="quick_operation">
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<param argument="--quick" type="select" label="Enable quick operation"
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help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
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<option value="yes">Yes</option>
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<option selected="True" value="no">No</option>
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</param>
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<when value="yes">
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<param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
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help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
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</when>
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<when value="no"/><!-- Do absolutely nothing -->
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</conditional>
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<param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
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label="Print no Kraken output for unclassified sequences"/>
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<expand macro="input_database" />
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</inputs>
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<outputs>
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<data name="classified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
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<filter>(split_reads)</filter>
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</data>
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<data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
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<filter>(split_reads)</filter>
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</data>
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<data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
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<!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
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</outputs>
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<tests>
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<test>
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<param name="single_paired_selector" value="no"/>
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<param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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<param name="split_reads" value="false"/>
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<param name="quick" value="no"/>
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<param name="only-classified-output" value="false"/>
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<param name="kraken_database" value="test_db"/>
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<output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
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</test>
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</tests>
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<help>
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<![CDATA[
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**What it does**
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Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.
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-----
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**Output Format**
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Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are::
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1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified.
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2. The sequence ID, obtained from the FASTA/FASTQ header.
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3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified.
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4. The length of the sequence in bp.
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5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
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a) the first 13 k-mers mapped to taxonomy ID #562
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b) the next 4 k-mers mapped to taxonomy ID #561
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c) the next 31 k-mers contained an ambiguous nucleotide
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d) the next k-mer was not in the database
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e) the last 3 k-mers mapped to taxonomy ID #562
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]]>
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</help>
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<expand macro="citations" />
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</tool>

‎tool_collections/kraken/kraken/macros.xml

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../macros.xml

‎tool_collections/kraken/kraken/test-data/kraken_test1.fa

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>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence
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CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAAC
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TCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCA
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ATGAAGCGGCGCACGAAAAACGCGAAAGCGT
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>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence
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CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGG
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AGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAA
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GCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT
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>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence
12+
TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGA
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AGCGGCGCACGAAAAACGCGAAAGCGT
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>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence
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GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTC
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ACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAA
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TCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCA
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TCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACC
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TAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTG
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TTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACC
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GGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTAT
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TGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTC
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TGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCA
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GCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAA
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CAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTT
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TTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGT
28+
TGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCAT
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GAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATA
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GGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATG
31+
AACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCG
32+
TTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAG
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TGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCG
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CTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTT
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CAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACT
36+
TCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCA
37+
TCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGAT
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TTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCT
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GCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCT
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GTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGG
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TTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACA
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AATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACG
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CGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGT
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AATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCG
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TGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCAT
46+
TCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTG
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CAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCT
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GGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTT
49+
TCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGG
50+
TCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTAC
51+
CCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCA
52+
GGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTC
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TACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAA
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ATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGA
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TTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAA
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CCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAA
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CACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATG
58+
ACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCA
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GGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC
60+
ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGG
61+
CGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCT
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TCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTC
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AAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGA
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TGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTAC
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TGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCG
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TACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTT
67+
TTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTG
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TTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACT
69+
ACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGAT
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TTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG

‎tool_collections/kraken/kraken/test-data/kraken_test1_output.tab

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C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162
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C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174
3+
C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88
4+
C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841

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