Mercurial > repos > jjkoehorst > sapp

comparison fasta2rdf.xml @ 35:fa736576c7ed draft

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planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
parents f2cbf1230026
children
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34:f2cbf1230026 35:fa736576c7ed
1 <tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1"> 1 <tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1">
2 <description>SAPP - FASTA 2 RDF conversion</description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container> 4 <container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container>
5 </requirements> 5 </requirements>
6 6 <command interpreter="docker">java -jar /fasta2rdf/FASTA2RDF-0.1-jar-with-dependencies.jar
7 <command>java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar
8 '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon' 7 '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon'
9 '--input' '$input' '--output' '$output' '-organism' '$organism' 8 '--input' '$input' '--output' '$output' '-organism' '$organism'
10 '--ncbi_taxid' '$ncbi_taxid' 9 '--ncbi_taxid' '$ncbi_taxid'
11 #if len(str($identification_tag))==0 10 #if len(str($identification_tag))==0
12 '--idtag' ${input.name} 11 '--idtag' ${input.name}
29 label="Select if it is a Genome/Gene/Protein or program wont start!"> 28 label="Select if it is a Genome/Gene/Protein or program wont start!">
30 <option value="">To be chosen</option> 29 <option value="">To be chosen</option>
31 <option value="genome"> Genome </option> 30 <option value="genome"> Genome </option>
32 <option value="gene"> Gene</option> 31 <option value="gene"> Gene</option>
33 <option value="protein"> Protein </option> 32 <option value="protein"> Protein </option>
34 <validator type="empty_field" message="Please select if it is a Genome, Gene or Protein" /> 33 <validator type="empty_field"
34 message="Please select if it is a Genome, Gene or Protein" />
35 </param> 35 </param>
36 </conditional> 36 </conditional>
37 37
38 <param name="table" type="select" label="Codon table"> 38 <param name="table" type="select" label="Codon table">
39 <option value="1"> 1 - UNIVERSAL </option> 39 <option value="1"> 1 - UNIVERSAL </option>