Mercurial > repos > iuc > seqtk
view seqtk_cutN.xml @ 3:bc7d99f46a5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author | iuc |
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date | Mon, 05 Jun 2017 13:27:11 -0400 |
parents | f73729b62b51 |
children | ecf1c30da3a2 |
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<?xml version="1.0"?> <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0"> <description>cut sequence at long N</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ seqtk cutN -n $n -p $p $g '$in_file' > '$default' ]]></command> <inputs> <expand macro="in_faq"/> <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" /> <param argument="-p" type="integer" value="10" label="Penalty for a non-N" /> <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" /> </inputs> <outputs> <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/> </outputs> <tests> <test> <param name="in_file" value="seqtk_cutn.fa"/> <param name="n" value="1"/> <output name="default" file="seqtk_cutn.out" ftype="fasta"/> </test> </tests> <help><![CDATA[ **What it does** Splits long sequences with runs of Ns :: >test AACTGATCGATCGATCGNNNNNNNNNNNACATG This will be split into the component sequences without the ambiguity. :: >test:1-17 AACTGATCGATCGATCG >test:29-33 ACATG @ATTRIBUTION@ ]]></help> <expand macro="citation" /> </tool>