Mercurial > repos > iuc > seqtk
view seqtk_comp.xml @ 8:3da72230c066 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author | iuc |
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date | Thu, 14 Oct 2021 09:22:39 +0000 |
parents | a09586d5149a |
children | 4b494533146a |
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<?xml version="1.0"?> <tool id="seqtk_comp" name="seqtk_comp" version="@TOOL_VERSION@.1"> <description>get the nucleotide composition of FASTA/Q</description> <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="@AWK_VERSION@">gawk</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ seqtk comp #if $in_bed: -r '$in_bed' #end if '$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' > '$default' ]]></command> <inputs> <expand macro="in_faq"/> <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/> </inputs> <outputs> <data name="default" format="tabular" label="Nucleotide composition of $in_file.name"/> </outputs> <tests> <test> <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/> <output name="default" file="seqtk_comp.out" ftype="tabular"/> </test> <test> <param name="in_file" value="seqtk_comp.fa.gz" ftype="fasta.gz"/> <output name="default" file="seqtk_comp.out" ftype="tabular"/> </test> </tests> <help><![CDATA[ **What it does** Reports composition of fasta/fastq sequences. For an example sequence like :: >test0 ACTGACTGAA >ambig_ref ACGTCGTGTTVHDBN The seqtk tool will report: :: #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts test0 11 4 2 2 2 0 0 1 0 0 0 0 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 @ATTRIBUTION@ ]]></help> <expand macro="citation" /> </tool>