Mercurial > repos > jjkoehorst > sapp
comparison fasta2rdf.xml @ 35:fa736576c7ed draft
planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author | jjkoehorst |
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date | Mon, 04 Jul 2016 10:37:59 -0400 |
parents | f2cbf1230026 |
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34:f2cbf1230026 | 35:fa736576c7ed |
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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> |