Mercurial > repos > iuc > seqtk
diff seqtk_mergefa.xml @ 3:bc7d99f46a5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author | iuc |
---|---|
date | Mon, 05 Jun 2017 13:27:11 -0400 |
parents | f73729b62b51 |
children | ecf1c30da3a2 |
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--- a/seqtk_mergefa.xml Fri Jan 01 14:49:42 2016 -0500 +++ b/seqtk_mergefa.xml Mon Jun 05 13:27:11 2017 -0400 @@ -1,47 +1,48 @@ <?xml version="1.0"?> <tool id="seqtk_mergefa" name="seqtk_mergefa" version="@WRAPPER_VERSION@.0"> - <description>merge two FASTA/Q files</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[seqtk mergefa -q $q + <description>merge two FASTA/Q files</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +seqtk mergefa +-q $q $i $m $r $h - -$in_fa1 -$in_fa2 - -> $default]]></command> - <inputs> - <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> - <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> - <param label="quality threshold" help="(-q)" name="q" type="integer" value="0"/> - <param checked="false" label="take intersection" help="(-i)" name="i" type="boolean" falsevalue="" truevalue="-i"/> - <param checked="false" label="convert to lowercase when one of the input base is N" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/> - <param checked="false" label="pick a random allele from het" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/> - <param checked="false" label="suppress hets in the input" help="(-h)" name="h" type="boolean" falsevalue="" truevalue="-h"/> - </inputs> - <outputs> - <data format_source="in_fa1" hidden="false" name="default" label="Merger of $in_fa1.name and $in_fa2.name"/> - </outputs> - <tests> - <test> - <param name="in_fa1" value="seqtk_mergefa1.fa"/> - <param name="in_fa2" value="seqtk_mergefa2.fa"/> - <output name="default" file="seqtk_mergefa.out" ftype="fasta"/> - </test> - <test> - <param name="in_fa1" value="seqtk_mergefa1.fa"/> - <param name="in_fa2" value="seqtk_mergefa2.fa"/> - <param name="m" value="True" /> - <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/> - </test> - </tests> - <help><![CDATA[ +'$in_fa1' +'$in_fa2' +> '$default' + ]]></command> + <inputs> + <param name="in_fa1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> + <param name="in_fa2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> + <param argument="-q" type="integer" value="0" label="Quality threshold"/> + <param argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Take intersection" /> + <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Convert to lowercase when one of the input base is N" /> + <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Pick a random allele from het" /> + <param argument="-h" type="boolean" truevalue="-h" falsevalue="" checked="false" label="Suppress hets in the input" /> + </inputs> + <outputs> + <data name="default" format_source="in_fa1" label="Merger of $in_fa1.name and $in_fa2.name"/> + </outputs> + <tests> + <test> + <param name="in_fa1" value="seqtk_mergefa1.fa"/> + <param name="in_fa2" value="seqtk_mergefa2.fa"/> + <output name="default" file="seqtk_mergefa.out" ftype="fasta"/> + </test> + <test> + <param name="in_fa1" value="seqtk_mergefa1.fa"/> + <param name="in_fa2" value="seqtk_mergefa2.fa"/> + <param name="m" value="True" /> + <output name="default" file="seqtk_mergefa2.out" ftype="fasta"/> + </test> + </tests> + <help><![CDATA[ **What it does** Merges two fasta files, using ambiguity codes @@ -64,6 +65,6 @@ ACTGACTGxxa @ATTRIBUTION@ -]]></help> - <expand macro="citation" /> + ]]></help> + <expand macro="citation" /> </tool>