Mercurial > repos > iuc > snap
view snap.xml @ 0:d398b2e6b2ff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author | iuc |
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date | Fri, 20 Oct 2017 03:52:36 -0400 |
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<tool id="snap" name="SNAP" profile="16.04" version="@VERSION@"> <description>gene prediction</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ snap -gff $lcmask #if $strand == 'forward' -plus #else if $strand == 'backward' -minus #end if -aa '${output_aa}' -tx '${output_tx}' '${model}' '${input_genome}' > '${output_gff}' ]]> </command> <inputs> <param name="input_genome" type="data" format="fasta" label="Genome Sequence"/> <param name="model" type="data" format="snaphmm" label="Prediction model" help="File created with 'Train SNAP' tool"/> <param argument="-lcmask" type="boolean" label="Treat lowercase as N" truevalue="-lcmask" falsevalue="" checked="false" /> <param name="strand" type="select" label="Predict genes on specific strands"> <option value="both">both</option> <option value="forward">forward</option> <option value="backward">backward</option> </param> </inputs> <outputs> <data format="gff" name="output_gff" label="${tool.name} on ${on_string}: GFF"/> <data format="fasta" name="output_aa" label="${tool.name} on ${on_string}: Protein sequence"/> <data format="fasta" name="output_tx" label="${tool.name} on ${on_string}: Coding sequence"/> </outputs> <tests> <test> <param name="input_genome" value="human.fa" ftype="fasta" /> <param name="model" value="snap.hmm" /> <!-- FIXME ftype temporarily removed because the not yet existing snaphmm type breaks travis tests --> <!--param name="model" value="snap.hmm" ftype="snaphmm" /--> <output name="output_gff" file="snap_annot.gff" ftype="gff"/> <output name="output_aa" file="annot_aa.fasta" ftype="fasta"/> <output name="output_tx" file="annot_tx.fasta" ftype="fasta"/> </test> </tests> <help> <![CDATA[ SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. ]]> </help> <expand macro="citations"/> </tool>