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comparison protein2rdf/protein_to_ttl.xml @ 12:0773b11fb822

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cutadapters added
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 16:56:49 +0100
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11:a712b378e090 12:0773b11fb822
1 <tool id="SAPP_protein_rdf" name="Protein FASTA to RDF" version="0.1">
2 <requirements>
3 <requirement type='package' version="3.4">python</requirement>
4 <requirement type='package' version="1.0">rdflib</requirement>
5 </requirements>
6 <description></description>
7 <command interpreter="python3.4">protein_to_ttl.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' '-diagnosis' '$diagnosis' '-country' '$country' '-location' '$location' '-date' '$date' -sourcedb SAPP
8 #for $index, $id in enumerate( $ids )
9 '-ids' '$id.id_tag'
10 #end for
11 '-id_alternative' '$input.name'
12 </command>
13 <inputs>
14 <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
15 <param size="60" name="organism" type="text" format="text" label="organism name"/>
16 <param size="60" name="diagnosis" type="text" format="text" label="Diagnosis of host if applicable"/>
17 <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
18 <param size="60" name="country" type="text" format="text" label="Country of sample"/>
19 <param size="60" name="location" type="text" format="text" label="Location of sample e.g., river, city, hospital"/>
20 <param size="60" name="date" type="text" format="text" label="Sample date"/>
21 <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!"/>
22 <repeat name="ids" title="Identification tags">
23 <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
24 </repeat>
25 </inputs>
26
27 <outputs>
28 <data format="rdf" name="output" label="proteinTTL: ${input.name}" />
29 </outputs>
30 <tests>
31 <test>
32 <param name="input" value="test-data/NC_017117.faa"/>
33 <output name="$output" file="NC_017117.rdf"/>
34 <output name="$ncbi_taxid" value="634455"/>
35 <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
36 <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
37 </test>
38 </tests>
39 <help>
40 RDF creation from a multi protein fasta file
41 </help>
42 </tool>