Mercurial > repos > diego > rtg_investigator
diff tools/rtg/format_fasta.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
---|---|
date | Sat, 21 Apr 2012 21:36:15 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rtg/format_fasta.xml Sat Apr 21 21:36:15 2012 -0400 @@ -0,0 +1,41 @@ +<tool id="rtg_format_fasta" name="Format FASTA"> + <description>to SDF with rtg format</description> + <command interpreter="bash">galaxy-rtg-wrapper.sh format +#if $paired.sPaired == "paired": +-l $paired.input1 +-r $paired.input2 +#else: +$paired.input1 +#end if +#if str($protein) == "true": +-p +#end if +-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="fasta" label="Source FASTA file"/> + </when> + <when value="paired"> + <param name="input1" type="data" format="fasta" label="First of pair FASTA file"/> + <param name="input2" type="data" format="fasta" label="Second of pairFASTA file"/> + </when> + </conditional> + <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 FASTA file to RTG SDF. + </help> + +</tool>