Mercurial > repos > iuc > transtermhp
diff transtermhp.xml @ 3:1a1ec22a7e28 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
| author | iuc |
|---|---|
| date | Wed, 07 Jun 2017 07:53:53 -0400 |
| parents | d763e35fef0b |
| children | 012171ba9fce |
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--- a/transtermhp.xml Fri Oct 09 09:40:48 2015 -0400 +++ b/transtermhp.xml Wed Jun 07 07:53:53 2017 -0400 @@ -1,27 +1,26 @@ -<?xml version="1.0"?> -<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0"> - <description>finds rho-independent transcription terminators in bacterial genomes</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[ +<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1"> + <description>finds rho-independent transcription terminators in bacterial genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ #if $reference_genome.source == 'history': - ln -s $reference_genome.genome_fasta genomeref.fa && + ln -s '$reference_genome.genome_fasta' genomeref.fa && #end if -python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT +python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP #if $reference_genome.source == 'cached': - "${reference_genome.fasta_indexes.fields.path}" + '${reference_genome.fasta_indexes.fields.path}' #elif $reference_genome.source == 'history': genomeref.fa #end if -$input_gff3 - -> $output]]></command> +'$input_gff3' +> '$output' + ]]></command> <inputs> <conditional name="reference_genome"> <param name="source" type="select" label="Reference Genome"> @@ -54,19 +53,19 @@ This is a TODO item that would be nice to get around to eventually (perhaps when a user demands it.) --> - </inputs> - <outputs> - <data format="gff3" name="output"/> - </outputs> - <tests> - <test> - <param name="source" value="history" /> - <param name="genome_fasta" value="sequence.fasta" /> - <param name="input_gff3" value="sequence.gff3" /> - <output name="output" file="sequence.gff3.out" /> - </test> - </tests> - <help><![CDATA[ + </inputs> + <outputs> + <data format="gff3" name="output"/> + </outputs> + <tests> + <test> + <param name="source" value="history" /> + <param name="genome_fasta" value="sequence.fasta" /> + <param name="input_gff3" value="sequence.gff3" /> + <output name="output" file="sequence.gff3.out" /> + </test> + </tests> + <help><![CDATA[ **What it does** Finds rho-independent transcription terminators in bacterial genomes.