Mercurial > repos > earlhaminst > smart_domains
diff smart_domains.xml @ 0:a3b26189fee3 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
author | earlhaminst |
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date | Thu, 15 Jun 2017 07:52:09 -0400 |
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children | 8c24cc7431aa |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_domains.xml Thu Jun 15 07:52:09 2017 -0400 @@ -0,0 +1,96 @@ +<tool id="smart_domains" name="SMART domains" version="0.1.0"> + <description>Search domains in protein sequences using SMART</description> + <requirements> + <requirement type="package" version="1.6.924">perl-bioperl</requirement> + <requirement type="package" version="2.90">perl-json</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +perl '$__tool_directory__/smart-domain.pl' +--inputFile='$inputFile' +$Pfam +$SignalP +$Repeats +$DISEMBL +$Schnipsel +$outputFormat + ]]></command> + <inputs> + <param name="inputFile" type="data" format="fasta" label="Protein sequences" help="In FASTA format" /> + <param name="Pfam" type="boolean" truevalue="--includePfam" falsevalue="" label="Include Pfam domains" argument="--includePfam" /> + <param name="SignalP" type="boolean" truevalue="--includeSignalP" falsevalue="" label="Include signal peptide predictions" argument="--includeSignalP" /> + <param name="Repeats" type="boolean" truevalue="--includeRepeats" falsevalue="" label="Include internal repeat predictions" argument="--includeRepeats" /> + <param name="DISEMBL" type="boolean" truevalue="--includeDISEMBL" falsevalue="" label="Include predictions of internal protein disorder" argument="--includeDISEMBL" /> + <param name="Schnipsel" type="boolean" truevalue="--includeSchnipsel" falsevalue="" label="Include predictions of outlier homologues and homologues of known structures" argument="--includeSchnipsel" /> + <param name="outputFormat" type="select" label="Output format"> + <option value="--outputFormat=txt" selected="true">Text</option> + <option value="--outputFormat=tabular">Tabular</option> + <option value="--outputFormat=json">JSON</option> + </param> + </inputs> + <outputs> + <collection name="output_lists" type="list" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<name>.+)_SMART_results\.(?P<ext>.+)" directory="SMART_results" /> + </collection> + </outputs> + <tests> + <test> + <param name="inputFile" ftype="fasta" value="seq.fa" /> + <param name="Pfam" value="true" /> + <param name="SignalP" value="false" /> + <param name="Repeats" value="false" /> + <param name="DISEMBL" value="false" /> + <param name="Schnipsel" value="false" /> + <param name="outputFormat" value="--outputFormat=txt" /> + <output_collection name="output_lists" type="list" count="12"> + <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.txt" ftype="txt" /> + <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.txt" ftype="txt" /> + <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.txt" ftype="txt" /> + <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.txt" ftype="txt" /> + <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.txt" ftype="txt" /> + <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.txt" ftype="txt" /> + <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.txt" ftype="txt" /> + <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.txt" ftype="txt" /> + <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.txt" ftype="txt" /> + <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.txt" ftype="txt" /> + <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.txt" ftype="txt" /> + <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.txt" ftype="txt" /> + </output_collection> + </test> + <test> + <param name="inputFile" ftype="fasta" value="seq.fa" /> + <param name="Pfam" value="true" /> + <param name="SignalP" value="false" /> + <param name="Repeats" value="false" /> + <param name="DISEMBL" value="false" /> + <param name="Schnipsel" value="false" /> + <param name="outputFormat" value="--outputFormat=json" /> + <output_collection name="output_lists" type="list" count="12"> + <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.json" ftype="json" compare="sim_size" /> + <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.json" ftype="json" compare="sim_size" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +A simple tool to search domains in multiple protein sequences contained in a FASTA file using the `SMART`_ web service. + +Written by Ivica Letunic <ivica@letunic.com> + +Modified by Anil Thanki <Anil.Thanki@earlham.ac.uk> to parse output in JSON and tabular format to adapt in Galaxy + +.. _SMART: http://smart.embl.de/ + ]]></help> + <citations> + <citation type="doi">10.1073/pnas.95.11.5857</citation> + <citation type="doi">10.1093/nar/gku949</citation> + </citations> +</tool>