Mercurial > repos > jjkoehorst > sapp
view conversion/fasta2rdf/fastatordf.xml @ 23:48fda68e50b1
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author | jjkoehorst <jasperkoehorst@gmail.com> |
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date | Sat, 21 Feb 2015 19:24:30 +0100 |
parents | 74b8ba5e2d5b |
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<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>