Mercurial > repos > iuc > barrnap
diff barrnap.xml @ 1:7355bbf5e05f draft
planemo upload commit 19a431ffca44dd1fd61ba2b66e5fc5ca96364f81
author | iuc |
---|---|
date | Sun, 10 Jun 2018 03:26:56 -0400 |
parents | 8fd427007e93 |
children | fe48aa4ccd5e |
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--- a/barrnap.xml Mon Aug 28 14:14:41 2017 -0400 +++ b/barrnap.xml Sun Jun 10 03:26:56 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="barrnap" name="barrnap" version="1.2.0"> +<tool id="barrnap" name="barrnap" version="1.2.1"> <description>Locate ribosomal RNA's in a fasta file. (GFF output)</description> <requirements> - <requirement type="package" version="0.8">barrnap</requirement> + <requirement type="package" version="0.9">barrnap</requirement> </requirements> <version_command>barrnap --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -14,6 +14,9 @@ #if $incseq --incseq #end if + #if $outseq + --outseq '$fasta_out' + #end if --kingdom $kingdom '$fasta_file' > '$gff' @@ -32,10 +35,14 @@ <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" /> <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" /> <param name="incseq" type="boolean" label="Include Sequences in GFF" help="Include the fasta sequences in the GFF output file" /> + <param name="outseq" type="boolean" label="Save rRNA hit seqs as FASTA" help="Produce an output file of the rRNA sequences found in FASTA format." /> </inputs> <outputs> <data name="gff" format="gff3" label="${tool.name} on ${on_string}: rRNA GFF"/> + <data name="fasta_out" format="fasta" label="${tool.name} on ${on_string}: rRNA Sequences"> + <filter>outseq</filter> + </data> </outputs> <tests> @@ -56,6 +63,13 @@ <param name="evalue" value="0.00000001" /> <output name="gff" value="test_3.gff" ftype="gff3" /> </test> + <test><!-- Test 4 --> + <param name="fasta_file" value="small.fna" ftype="fasta" /> + <param name="outseq" value="true" /> + <param name="kingdom" value="bac" /> + <output name="gff" value="test_4.gff" ftype="gff3" /> + <output name="fasta_out" value="test_4.fna" ftype="fasta" /> + </test> </tests> <help>