Mercurial > repos > jjkoehorst > sapp
diff conversion/fasta2rdf/fastatordf.xml @ 16:74b8ba5e2d5b
aragorn addition
| author | jjkoehorst <jasperkoehorst@gmail.com> |
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| date | Sat, 21 Feb 2015 17:17:06 +0100 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conversion/fasta2rdf/fastatordf.xml Sat Feb 21 17:17:06 2015 +0100 @@ -0,0 +1,38 @@ +<tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1"> + <requirements> + <requirement type='package' version="3.4">python</requirement> + <requirement type='package' version="1.0">rdflib</requirement> + </requirements> + <description></description> + <command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -sourcedb SAPP + #for $index, $id in enumerate( $ids ) + '-ids' '$id.id_tag' + #end for + '-id_alternative' '$input.name' + </command> + <inputs> + <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/> + <param size="60" name="organism" type="text" format="text" label="organism name" optional="false"/> + <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/> + <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"/> + <repeat name="ids" title="Identification tags"> + <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/> + </repeat> + </inputs> + + <outputs> + <data format="rdf" name="output" label="genomeTTL: ${input.name}" /> + </outputs> + + <tests> + <test> + <param name="input" value="test-data/NC_017117.fna"/> + <output name="$output" file="NC_017117.rdf"/> + <output name="$ncbi_taxid" value="634455"/> + <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/> + <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/> + </test> + </tests> + +<help> Genome FASTA file to RDF</help> +</tool>