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Added the profile2cami tool, a component of the TaxonKit suite. #6085
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name: taxonkit | ||
owner: iuc | ||
description: TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit | ||
homepage_url: https://bioinf.shenwei.me/taxonkit/ | ||
long_description: | | ||
TaxonKit is a set of tools for analyzing and manipulating taxonomic data. It includes utilities for converting metagenomic profile tables to CAMI format, among other functionalities. | ||
remote_repository_url: https://github.com/shenwei356/taxonkit | ||
categories: | ||
- Metagenomics | ||
type: unrestricted | ||
auto_tool_repositories: | ||
name_template: "{{ tool_id }}" | ||
description_template: "Wrapper for TaxonKit function: {{ tool_name }}." | ||
suite: | ||
name: "suite_taxonkit" | ||
description: "A suite of tools that brings the TaxonKit project into Galaxy." | ||
long_description: | | ||
TaxonKit is a set of tools for analyzing and manipulating taxonomic data, including converting metagenomic profile tables to CAMI format. |
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<macros> | ||
<xml name="requirements"> | ||
<requirements> | ||
<requirement type="package" version="@TOOL_VERSION@">taxonkit</requirement> | ||
<yield/> | ||
</requirements> | ||
</xml> | ||
<token name="@TOOL_VERSION@">0.17.0</token> | ||
<token name="@VERSION_SUFFIX@">0</token> | ||
<token name="@PROFILE@">21.05</token> | ||
<xml name="biotools"> | ||
<xrefs> | ||
<xref type="bio.tools">taxonkit</xref> | ||
</xrefs> | ||
</xml> | ||
<xml name="citations"> | ||
<citations> | ||
<citation type="doi">10.1016/j.jgg.2021.03.006</citation> | ||
<yield/> | ||
</citations> | ||
</xml> | ||
</macros> |
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<tool id="profile2cami" name="Profile2CAMI" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
<description>Convert metagenomic profile table to CAMI format</description> | ||
<macros> | ||
<import>macros.xml</import> | ||
</macros> | ||
<expand macro="biotools"/> | ||
<expand macro="requirements" /> | ||
<command detect_errors="exit_code"> | ||
<![CDATA[ | ||
taxonkit profile2cami | ||
--data-dir '${taxonomy.fields.path}' | ||
--abundance-field '${abundance_field}' | ||
--taxid-field '${taxid_field}' | ||
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$percentage | ||
$recompute_abd | ||
$keep_zero | ||
$no_sum_up | ||
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#if $sample_id: | ||
-s '${sample_id}' | ||
#end if | ||
#if $taxonomy_id: | ||
-t '${taxonomy_id}' | ||
#end if | ||
--show-rank '${ranks}' | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. can you put this in an if condition, so that if nothing is selected, all ranks are used as is the default by the tool ? also, please adjust the test for it, that's more convenient for the user |
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${input_file} | ||
> '${cami_output}' | ||
]]> | ||
</command> | ||
<inputs> | ||
<param name="input_file" type="data" format="txt" label="Input Profile File" help="A tab-delimited profile file with TaxId and abundance columns." /> | ||
<param argument="--taxonomy" type="select" label="NCBI taxonomy" help="This NCBI database is used to map human-readable taxon names to TaxId's."> | ||
<options from_data_table="ncbi_taxonomy"> | ||
<validator message="No NCBI database is available" type="no_options"/> | ||
</options> | ||
</param> | ||
<param name="abundance_field" type="integer" value="2" label="Abundance Field Index" help="Field index of abundance in the input data." /> | ||
<param name="taxid_field" type="integer" value="1" label="TaxId Field Index" help="Field index of TaxId in the input data." /> | ||
<param name="percentage" type="boolean" value="false" label="Abundance in Percentage" help="Check if the abundance values are in percentage." truevalue="-p" falsevalue=""/> | ||
<param name="recompute_abd" type="boolean" value="false" label="Recompute Abundance" help="Check to recompute abundance if some TaxIds are deleted in the current taxonomy version." truevalue="-R" falsevalue=""/> | ||
<param name="keep_zero" type="boolean" value="false" label="Keep Zero Abundances" help="Check to keep taxons with abundance of zero." truevalue="-0" falsevalue=""/> | ||
<param name="no_sum_up" type="boolean" value="false" label="Do Not Sum Up Abundance" help="Do not sum up abundance from child to parent TaxIds." truevalue="-S" falsevalue="" /> | ||
<param name="sample_id" type="text" value="" label="Sample ID" help="Optional sample ID to include in the result file." /> | ||
<param name="taxonomy_id" type="text" value="" label="Taxonomy ID" help="Optional taxonomy ID to include in the result file." /> | ||
<param name ="ranks" argument="--show-rank" type="select" multiple="true" label="Show Ranks" help="Specify the ranks to show in the result file."> | ||
<option value="superkingdom">Superkingdom</option> | ||
<option value="phylum">Phylum</option> | ||
<option value="class">Class</option> | ||
<option value="order">Order</option> | ||
<option value="family">Family</option> | ||
<option value="genus">Genus</option> | ||
<option value="species">Species</option> | ||
<option value="strain">Strain</option> | ||
</param> | ||
</inputs> | ||
<outputs> | ||
<data name="cami_output" format="tsv" label="Converted CAMI Output" /> | ||
</outputs> | ||
<tests> | ||
<!-- Test 1: Basic functionality with default parameters --> | ||
<test expect_num_outputs="1"> | ||
<param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
<param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
<output name="cami_output" file="output1_basic_functionality.tsv" /> | ||
</test> | ||
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<!-- Test 2: Using percentage flag --> | ||
<test expect_num_outputs="1"> | ||
<param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
<param name="percentage" value="true" /> | ||
<param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
<output name="cami_output" file="output2_percentage_flag.tsv" /> | ||
</test> | ||
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<!-- Test 3: Recomputing abundance with deleted TaxIds --> | ||
<test expect_num_outputs="1"> | ||
<param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
<param name="recompute_abd" value="true" /> | ||
<param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
<output name="cami_output" file="output3_recompute_abd.tsv" /> | ||
</test> | ||
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<!-- Test 4: Profile2Cami with all parameters checked --> | ||
<test expect_num_outputs="1"> | ||
<param name="input_file" value="abundance.tsv" ftype="tsv" /> | ||
<param name="percentage" value="true" /> | ||
<param name="recompute_abd" value="true" /> | ||
<param name="keep_zero" value="true" /> | ||
<param name="no_sum_up" value="true" /> | ||
<param name="ranks" value="superkingdom,phylum,class,order,family,genus,species,strain" /> | ||
<output name="cami_output" file="output4_all_param.tsv" /> | ||
</test> | ||
</tests> | ||
<help> | ||
<![CDATA[ | ||
**What is Profile2CAMI** | ||
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Profile2CAMI is a tool for converting metagenomic profile tables to CAMI format. | ||
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**Inputs** | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. All info that is given in the input parameters can be removed from the help |
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- A tab-delimited profile file with TaxId and abundance columns. | ||
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**Outputs** | ||
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- A CAMI formatted file. | ||
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For more information, please refer to the tool's documentation. | ||
]]> | ||
</help> | ||
<expand macro="citations" /> | ||
</tool> |
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83333 0.2 merged to 562 | ||
83333 0.2 absord 562 | ||
561 0.5 no change | ||
91347 0.1 deleted |
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test-db-tox Test Database ${__HERE__}/test-db |
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@SampleID: | ||
@Version:0.10.0 | ||
@Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
@TaxonomyID: | ||
@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
2 superkingdom 2 Bacteria 100.000000000000000 | ||
1224 phylum 2|1224 Bacteria|Proteobacteria 100.000000000000000 | ||
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 100.000000000000000 | ||
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 100.000000000000000 | ||
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 90.000000000000000 | ||
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 90.000000000000000 | ||
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000000 |
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@SampleID: | ||
@Version:0.10.0 | ||
@Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
@TaxonomyID: | ||
@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
2 superkingdom 2 Bacteria 1.000000000000000 | ||
1224 phylum 2|1224 Bacteria|Proteobacteria 1.000000000000000 | ||
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 1.000000000000000 | ||
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 1.000000000000000 | ||
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 0.900000000000000 | ||
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 0.900000000000000 | ||
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 0.400000000000000 |
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@SampleID: | ||
@Version:0.10.0 | ||
@Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
@TaxonomyID: | ||
@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
2 superkingdom 2 Bacteria 190.000000000000000 | ||
1224 phylum 2|1224 Bacteria|Proteobacteria 190.000000000000000 | ||
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 190.000000000000000 | ||
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 190.000000000000000 | ||
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 90.000000000000000 | ||
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 90.000000000000000 | ||
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 40.000000000000000 |
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@SampleID: | ||
@Version:0.10.0 | ||
@Ranks:superkingdom|phylum|class|order|family|genus|species|strain | ||
@TaxonomyID: | ||
@@TAXID RANK TAXPATH TAXPATHSN PERCENTAGE | ||
2 superkingdom 2 Bacteria 0.500000000000000 | ||
1224 phylum 2|1224 Bacteria|Proteobacteria 0.500000000000000 | ||
1236 class 2|1224|1236 Bacteria|Proteobacteria|Gammaproteobacteria 0.500000000000000 | ||
91347 order 2|1224|1236|91347 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales 0.500000000000000 | ||
543 family 2|1224|1236|91347|543 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae 0.500000000000000 | ||
561 genus 2|1224|1236|91347|543|561 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia 0.500000000000000 | ||
562 species 2|1224|1236|91347|543|561|562 Bacteria|Proteobacteria|Gammaproteobacteria|Enterobacteriales|Enterobacteriaceae|Escherichia|Escherichia coli 0.400000000000000 |
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Please add bio.tool xml: https://bio.tools/taxonkit