Mercurial > repos > diego > rtg_investigator
view tools/rtg/format_fastq.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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<tool id="rtg_format_fastq" name="Format FASTQ"> <description>to SDF with rtg format</description> <command interpreter="bash">galaxy-rtg-wrapper.sh format -f fastq #if $paired.sPaired == "paired": -l $paired.input1 -r $paired.input2 #else: $paired.input1 #end if #if str($protein) == "true": -p #end if -q $quality_format -o ${output.extra_files_path} >$output</command> <inputs> <conditional name="paired"> <param name="sPaired" type="select" label="Are you formatting paired-end reads?"> <option value="single">Non-read data or single-end</option> <option value="paired">Paired-end</option> </param> <when value="single"> <param name="input1" type="data" format="fastq" label="Source FASTQ file"/> </when> <when value="paired"> <param name="input1" type="data" format="fastq" label="First of pair FASTA file"/> <param name="input2" type="data" format="fastq" label="Second of pair FASTA file"/> </when> </conditional> <param name="quality_format" type="select" label="Quality format"> <option value="sanger" selected="true">Sanger</option> <option value="solexa">Solexa</option> <option value="illumina">Illumina</option> </param> <param name="protein" type="select" label="Input consists of protein"> <option value="false" selected="true">False</option> <option value="true">True</option> </param> </inputs> <outputs> <data format="rtg_sdf" name="output" /> </outputs> <help> This tool formats a FASTQ file to RTG SDF. </help> </tool>