Mercurial > repos > stheil > idba_ud_wrapper
view fq2fa.xml @ 2:edda44d54b59 draft default tip
Uploaded
author | stheil |
---|---|
date | Fri, 16 Oct 2015 04:16:19 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="fq2fa" name="fq2fa" version="1.1.1 (Oct 18, 2012)"> <description>fq2fa is a simple tool given by IDBA package that allows to convert fastq to fasta, merge paired-end reads and filter out reads containing 'N's</description> <command> fq2fa #if $fileLayout.layout=='paired' --paired $fileLayout.sequence #else if $fileLayout.layout=='merge' --merge $fileLayout.sequenceR1 $fileLayout.sequenceR2 #else $fileLayout.sequence #end if $filter $output </command> <inputs> <conditional name="fileLayout"> <param name="layout" type="select" label="File layout"> <option value="">single end</option> <option value="paired">paired-end in one file</option> <option value="merge">paired-end in two files</option> </param> <when value=""> <param name="sequence" type="data" format="fastq" label="Single sequence file"/> </when> <when value="--paired"> <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/> </when> <when value="--merge"> <param name="sequenceR1" type="data" format="fastq" label="Forward sequence file (R1)"/> <param name="sequenceR2" type="data" format="fastq" label="Reverse sequence file (R2)"/> </when> </conditional> <param name="filter" type="boolean" checked="false" truevalue="--filter" falsevalue="" label="Filter out reads containing 'N'"/> </inputs> <outputs> <data name="output" format="fasta" label="Fasta from fq2fa"/> </outputs> <help> ===== fq2fa ===== Convert Fastq sequences to Fasta sequences. | ``Usage:`` | ``fq2fa tmp.fq tmp.fa [...]`` | ``fq2fa --paired tmp.fq tmp.fa`` | ``fq2fa --merge tmp_1.fq tmp_2.fq tmp.fa`` | | Allowed Options: --paired if the reads are paired-end in one file --merge if the reads are paired-end in two files --filter filter out reads containing 'N' </help> </tool>