comparison fasta2rdf/fastatordf.xml @ 7:c79025539d9b

FASTA to RDF
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 15:23:15 +0100
parents ec73c34af97b
children 0773b11fb822
comparison
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5:e159dbecdad6 7:c79025539d9b
1 <tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1">
2 <description></description>
3 <command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -sourcedb SAPP
4 #for $index, $id in enumerate( $ids )
5 '-ids' '$id.id_tag'
6 #end for
7 '-id_alternative' '$input.name'
8 </command>
9 <inputs>
10 <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
11 <param size="60" name="organism" type="text" format="text" label="organism name" optional="false"/>
12 <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
13 <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!" optional="false"/>
14 <repeat name="ids" title="Identification tags">
15 <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
16 </repeat>
17 </inputs>
18
19 <outputs>
20 <data format="rdf" name="output" label="genomeTTL: ${input.name}" />
21 </outputs>
22
23 <tests>
24 <test>
25 <param name="input" value="test-data/NC_017117.fna"/>
26 <output name="$output" file="NC_017117.rdf"/>
27 <output name="$ncbi_taxid" value="634455"/>
28 <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
29 <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
30 </test>
31 </tests>
32
33 <help> Genome FASTA file to RDF</help>
34 </tool>