Mercurial > repos > iracooke > protk_proteogenomics
view protxml_to_gff.xml @ 1:a85c8de9630a draft
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author | iracooke |
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date | Thu, 26 Mar 2015 20:16:00 -0400 |
parents | 28067ed4ea0e |
children | 68d8c9e521d7 |
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<tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0"> <description>Export Proteomics Data to GFF</description> <requirements> <container type="docker">iracooke/protk-1.4.1</container> <requirement type="package" version="1.4">protk</requirement> <requirement type="package" version="2.2.29">blast+</requirement> </requirements> <command> protxml_to_gff.rb $protxml_file #if $database.source_select=="built_in": -d $database.dbkey #else -d $database.fasta_file #end if -c $gene_file --gff-idregex='$gffidpattern' -o $output </command> <stdio> <exit_code range="1:" level="fatal" description="Failure" /> </stdio> <inputs> <conditional name="database"> <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file"> <option value="input_ref">Your Upload File</option> <option value="built_in">Built-In</option> </param> <when value="built_in"> <param name="dbkey" type="select" format="text" > <label>Database</label> <options from_file="pepxml_databases.loc"> <column name="name" index="0" /> <column name="value" index="2" /> </options> </param> </when> <when value="input_ref"> <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" /> </when> </conditional> <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/> <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/> <param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> </valid> <mapping initial="none"> <add source="'" target="__sq__"/> </mapping> </sanitizer> </param> </inputs> <outputs> <data format="gff3" name="output" /> </outputs> <tests> <test> <param name="source_select" value="input_ref"/> <param name="fasta_file" value="small_prot.fasta" format="fasta"/> <param name="protxml_file" value="small.prot.xml" format="protxml"/> <param name="gene_file" value="small_combined.gff" format="gff3"/> <output name="output" format="gff3"> <assert_contents> <has_text text="polypeptide" /> </assert_contents> </output> </test> </tests> <help> **What it does** Exports peptides and proteins to gff ---- **References** </help> </tool>