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Merged
merged 19 commits into from
Jan 28, 2017
Merged

migrate in emboss_5, fastqc, freebayes, picard from devteam #1109

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94a8979
migrate in emboss_5, fastqc, freebayes, picard from devteam
martenson Jan 11, 2017
db5485d
replace links to docs, now self hosted by iuc since owners removed 5.…
martenson Jan 11, 2017
7a6f0e6
fix some more doc URLs manually
martenson Jan 11, 2017
f0ec210
add .gz file needed for fastqc test that was ignore by .gitignote
martenson Jan 11, 2017
9c22360
FreeBayes: update to leftalign
yhoogstrate Jan 17, 2017
c705c27
few minor chanes to FreeBayes
yhoogstrate Jan 17, 2017
81d2d6f
few minor chanes to FreeBayes
yhoogstrate Jan 17, 2017
b900a80
Fix flake8 errors
nsoranzo Jan 17, 2017
33ff2fe
dos2unix
nsoranzo Jan 17, 2017
cafb44d
Lint and clean-ups
nsoranzo Jan 19, 2017
10954c0
Add macros/read_group_macros.xml for Picard tools
nsoranzo Jan 19, 2017
b41af25
Merge pull request #1 from yhoogstrate/migrate-chosen-devteam-tools
martenson Jan 20, 2017
35ac630
Small fixes to freebayes wrappers
nsoranzo Jan 20, 2017
e468d37
FreeBayes: quotes
yhoogstrate Jan 23, 2017
78ee1ad
minor fastq updates
yhoogstrate Jan 23, 2017
6595b0a
FastQC: revert tool version
yhoogstrate Jan 24, 2017
d38e1e7
Fix mismatched quote
nsoranzo Jan 27, 2017
4e80a60
Fix raw string for Python3
nsoranzo Jan 27, 2017
1b20afe
remove JAVA_HOME from env
bgruening Jan 28, 2017
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8 changes: 8 additions & 0 deletions tools/emboss_5/.shed.yml
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categories:
- Sequence Analysis
- Fasta Manipulation
description: Galaxy wrappers for Emboss version 5.0.0 tools
name: emboss_5
owner: devteam
remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5
type: unrestricted
58 changes: 58 additions & 0 deletions tools/emboss_5/emboss_antigenic.xml
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<tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0">
<description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
<command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>On query</label>
</param>
<param name="minlen" type="text" value="6">
<label>Minimum Length of region</label>
</param>
<param name="out_format1" type="select">
<label>Output format</label>
<option value="gff">GFF</option>
<option value="pir">PIR</option>
<option value="swiss">SwissProt</option>
<option value="dbmotif">DbMotif</option>
<option value="diffseq">diffseq</option>
<option value="excel">Excel (TAB Delimited)</option>
<option value="feattable">FeatTable</option>
<option value="motif">Motif</option>
<option value="nametable">NameTable</option>
<option value="regions">Regions</option>
<option value="seqtable">SeqTable</option>
<option value="simple">SRS simple</option>
<option value="srs">SRS</option>
<option value="table">Table</option>
<option value="tagseq">Tagseq</option>
<option value="antigenic">Antigenic Output File</option>
</param>
</inputs>
<outputs>
<data format="antigenic" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="minlen" value="6"/>
<param name="out_format1" value="excel"/>
<output name="out_file1" file="emboss_antigenic_out.tabular"/>
</test>
</tests>
<code file="emboss_format_corrector.py" />
<help>
You can view the original documentation here_.

.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/antigenic.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_

</help>
</tool>
228 changes: 228 additions & 0 deletions tools/emboss_5/emboss_backtranseq.xml
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<tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0">
<description>Back translate a protein sequence</description>
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
<command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command>
<inputs>
<param format="fasta" name="input1" type="data">
<label>On query</label>
</param>
<param name="cfile" type="select">
<label>Codon Usage File</label>
<option value="Ehum.cut">Ehum.cut</option>
<option value="Eacc.cut">Eacc.cut</option>
<option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
<option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
<option value="Eaidlav.cut">Eaidlav.cut</option>
<option value="Eanasp.cut">Eanasp.cut</option>
<option value="Eani.cut">Eani.cut</option>
<option value="Eani_h.cut">Eani_h.cut</option>
<option value="Eanidmit.cut">Eanidmit.cut</option>
<option value="Easn.cut">Easn.cut</option>
<option value="Eath.cut">Eath.cut</option>
<option value="Eatu.cut">Eatu.cut</option>
<option value="Eavi.cut">Eavi.cut</option>
<option value="Ebja.cut">Ebja.cut</option>
<option value="Ebly.cut">Ebly.cut</option>
<option value="Ebme.cut">Ebme.cut</option>
<option value="Ebmo.cut">Ebmo.cut</option>
<option value="Ebna.cut">Ebna.cut</option>
<option value="Ebov.cut">Ebov.cut</option>
<option value="Ebovsp.cut">Ebovsp.cut</option>
<option value="Ebst.cut">Ebst.cut</option>
<option value="Ebsu.cut">Ebsu.cut</option>
<option value="Ebsu_h.cut">Ebsu_h.cut</option>
<option value="Ecac.cut">Ecac.cut</option>
<option value="Ecal.cut">Ecal.cut</option>
<option value="Eccr.cut">Eccr.cut</option>
<option value="Ecel.cut">Ecel.cut</option>
<option value="Echi.cut">Echi.cut</option>
<option value="Echicken.cut">Echicken.cut</option>
<option value="Echisp.cut">Echisp.cut</option>
<option value="Echk.cut">Echk.cut</option>
<option value="Echmp.cut">Echmp.cut</option>
<option value="Echnt.cut">Echnt.cut</option>
<option value="Echos.cut">Echos.cut</option>
<option value="Echzm.cut">Echzm.cut</option>
<option value="Echzmrubp.cut">Echzmrubp.cut</option>
<option value="Ecpx.cut">Ecpx.cut</option>
<option value="Ecre.cut">Ecre.cut</option>
<option value="Ecrisp.cut">Ecrisp.cut</option>
<option value="Ectr.cut">Ectr.cut</option>
<option value="Edayhoff.cut">Edayhoff.cut</option>
<option value="Eddi.cut">Eddi.cut</option>
<option value="Eddi_h.cut">Eddi_h.cut</option>
<option value="Edog.cut">Edog.cut</option>
<option value="Edro.cut">Edro.cut</option>
<option value="Edro_h.cut">Edro_h.cut</option>
<option value="Edrosophila.cut">Edrosophila.cut</option>
<option value="Eeca.cut">Eeca.cut</option>
<option value="Eeco.cut">Eeco.cut</option>
<option value="Eeco_h.cut">Eeco_h.cut</option>
<option value="Eecoli.cut">Eecoli.cut</option>
<option value="Ef1.cut">Ef1.cut</option>
<option value="Efish.cut">Efish.cut</option>
<option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
<option value="Eham.cut">Eham.cut</option>
<option value="Ehha.cut">Ehha.cut</option>
<option value="Ehin.cut">Ehin.cut</option>
<option value="Ehma.cut">Ehma.cut</option>
<option value="Ehuman.cut">Ehuman.cut</option>
<option value="Ekla.cut">Ekla.cut</option>
<option value="Ekpn.cut">Ekpn.cut</option>
<option value="Ella.cut">Ella.cut</option>
<option value="Emac.cut">Emac.cut</option>
<option value="Emaize.cut">Emaize.cut</option>
<option value="Emam_h.cut">Emam_h.cut</option>
<option value="Emixlg.cut">Emixlg.cut</option>
<option value="Emouse.cut">Emouse.cut</option>
<option value="Emsa.cut">Emsa.cut</option>
<option value="Emse.cut">Emse.cut</option>
<option value="Emta.cut">Emta.cut</option>
<option value="Emtu.cut">Emtu.cut</option>
<option value="Emus.cut">Emus.cut</option>
<option value="Emussp.cut">Emussp.cut</option>
<option value="Emva.cut">Emva.cut</option>
<option value="Emze.cut">Emze.cut</option>
<option value="Emzecp.cut">Emzecp.cut</option>
<option value="Encr.cut">Encr.cut</option>
<option value="Eneu.cut">Eneu.cut</option>
<option value="Engo.cut">Engo.cut</option>
<option value="Eoncsp.cut">Eoncsp.cut</option>
<option value="Epae.cut">Epae.cut</option>
<option value="Epea.cut">Epea.cut</option>
<option value="Epet.cut">Epet.cut</option>
<option value="Epfa.cut">Epfa.cut</option>
<option value="Ephix174.cut">Ephix174.cut</option>
<option value="Ephv.cut">Ephv.cut</option>
<option value="Ephy.cut">Ephy.cut</option>
<option value="Epig.cut">Epig.cut</option>
<option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
<option value="Epombe.cut">Epombe.cut</option>
<option value="Epombecai.cut">Epombecai.cut</option>
<option value="Epot.cut">Epot.cut</option>
<option value="Eppu.cut">Eppu.cut</option>
<option value="Epse.cut">Epse.cut</option>
<option value="Epsy.cut">Epsy.cut</option>
<option value="Epvu.cut">Epvu.cut</option>
<option value="Erab.cut">Erab.cut</option>
<option value="Erabbit.cut">Erabbit.cut</option>
<option value="Erabsp.cut">Erabsp.cut</option>
<option value="Erat.cut">Erat.cut</option>
<option value="Eratsp.cut">Eratsp.cut</option>
<option value="Erca.cut">Erca.cut</option>
<option value="Erhm.cut">Erhm.cut</option>
<option value="Eric.cut">Eric.cut</option>
<option value="Erle.cut">Erle.cut</option>
<option value="Erme.cut">Erme.cut</option>
<option value="Ersp.cut">Ersp.cut</option>
<option value="Esalsp.cut">Esalsp.cut</option>
<option value="Esau.cut">Esau.cut</option>
<option value="Esco.cut">Esco.cut</option>
<option value="Esgi.cut">Esgi.cut</option>
<option value="Eshp.cut">Eshp.cut</option>
<option value="Eshpsp.cut">Eshpsp.cut</option>
<option value="Esli.cut">Esli.cut</option>
<option value="Eslm.cut">Eslm.cut</option>
<option value="Esma.cut">Esma.cut</option>
<option value="Esmi.cut">Esmi.cut</option>
<option value="Esmu.cut">Esmu.cut</option>
<option value="Esoy.cut">Esoy.cut</option>
<option value="Espi.cut">Espi.cut</option>
<option value="Espn.cut">Espn.cut</option>
<option value="Espo.cut">Espo.cut</option>
<option value="Espo_h.cut">Espo_h.cut</option>
<option value="Espu.cut">Espu.cut</option>
<option value="Esta.cut">Esta.cut</option>
<option value="Esty.cut">Esty.cut</option>
<option value="Esus.cut">Esus.cut</option>
<option value="Esv40.cut">Esv40.cut</option>
<option value="Esyhsp.cut">Esyhsp.cut</option>
<option value="Esynsp.cut">Esynsp.cut</option>
<option value="Etbr.cut">Etbr.cut</option>
<option value="Etcr.cut">Etcr.cut</option>
<option value="Eter.cut">Eter.cut</option>
<option value="Etetsp.cut">Etetsp.cut</option>
<option value="Etob.cut">Etob.cut</option>
<option value="Etobcp.cut">Etobcp.cut</option>
<option value="Etom.cut">Etom.cut</option>
<option value="Etrb.cut">Etrb.cut</option>
<option value="Evco.cut">Evco.cut</option>
<option value="Ewht.cut">Ewht.cut</option>
<option value="Exel.cut">Exel.cut</option>
<option value="Exenopus.cut">Exenopus.cut</option>
<option value="Eyeast.cut">Eyeast.cut</option>
<option value="Eyeastcai.cut">Eyeastcai.cut</option>
<option value="Eyen.cut">Eyen.cut</option>
<option value="Eysc.cut">Eysc.cut</option>
<option value="Eysc_h.cut">Eysc_h.cut</option>
<option value="Eyscmt.cut">Eyscmt.cut</option>
<option value="Eysp.cut">Eysp.cut</option>
<option value="Ezebrafish.cut">Ezebrafish.cut</option>
<option value="Ezma.cut">Ezma.cut</option>
</param>
<param name="out_format1" type="select">
<label>Output Sequence File Format</label>
<option value="fasta">FASTA (m)</option>
<option value="acedb">ACeDB (m)</option>
<option value="asn1">ASN.1 (m)</option>
<option value="clustal">Clustal (m)</option>
<option value="codata">CODATA (m)</option>
<option value="embl">EMBL (m)</option>
<option value="fitch">Fitch (m)</option>
<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
<option value="genbank">GENBANK (m)</option>
<option value="gff">GFF (m)</option>
<option value="hennig86">Hennig86 (m)</option>
<option value="ig">Intelligenetics (m)</option>
<option value="jackknifer">Jackknifer (m)</option>
<option value="jackknifernon">Jackknifernon (m)</option>
<option value="mega">Mega (m)</option>
<option value="meganon">Meganon (m)</option>
<option value="msf">Wisconsin Package GCG's MSF (m)</option>
<option value="pir">NBRF (PIR) (m)</option>
<option value="ncbi">NCBI style FASTA (m)</option>
<option value="nexus">Nexus/PAUP (m)</option>
<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
<option value="phylip">PHYLIP interleaved (m)</option>
<option value="phylipnon">PHYLIP non-interleaved (m)</option>
<option value="selex">SELEX (m)</option>
<option value="staden">Staden (s)</option>
<option value="strider">DNA strider (m)</option>
<option value="swiss">SwisProt entry (m)</option>
<option value="text">Plain sequence (s)</option>
<option value="treecon">Treecon (m)</option>
</param>
</inputs>
<outputs>
<data format="txt" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<param name="cfile" value="Ehum.cut"/>
<param name="out_format1" value="fasta"/>
<output name="out_file1" file="emboss_backtranseq_out.fasta"/>
</test>
</tests>
<code file="emboss_format_corrector.py" />
<help>

.. class:: warningmark

The input dataset needs to be sequences.

-----

You can view the original documentation here_.

.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/backtranseq.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
</help>
</tool>
16 changes: 16 additions & 0 deletions tools/emboss_5/emboss_banana.pl
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#! /usr/bin/perl -w
use strict;

my $cmd_string = join (" ",@ARGV);
#my $cmd_string = "/home/djb396/temp/emboss/bin/banana -sequence /home/djb396/universe-prototype/test.fasta -outfile result.txt -graph png -goutfile results -auto";
my $results = `$cmd_string`;
my @files = split("\n",$results);
foreach my $thisLine (@files)
{
if ($thisLine =~ /Created /i)
{
$thisLine =~ /[\w|\.]+$/;
$thisLine =$&;
print "outfile: $thisLine\n";
}
}
32 changes: 32 additions & 0 deletions tools/emboss_5/emboss_banana.xml
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<tool id="EMBOSS: banana3" name="banana" version="5.0.0">
<description>Bending and curvature plot in B-DNA</description>
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
<command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command>
<inputs>
<param format="data" name="input1" type="data">
<label>On query</label>
</param>
</inputs>
<outputs>
<data format="txt" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="2.fasta"/>
<output name="out_file1" file="emboss_banana_out.txt"/>
</test>
</tests>
<help>
You can view the original documentation here_.

.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/banana.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
</help>
</tool>
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