Mercurial > repos > diego > rtg_investigator
diff tools/rtg/map.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rtg/map.xml Sat Apr 21 21:36:15 2012 -0400 @@ -0,0 +1,55 @@ +<tool id="rtg_map" name="Map"> + <description>reads with rtg map</description> + <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__ +map -t ${template.extra_files_path} +--repeat-freq ${repeat} +-i ${reads.extra_files_path} +#if $paired.sPaired == "paired": +--min-insert-size $paired.minlength --max-insert-size $paired.maxlength +--max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore +#else: +--max-alignment-score $paired.maxscore +#end if +</command> + <inputs> + <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/> + <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/> + <param name="repeat" type="text" value="90%" label="Repeat frequency"> + <sanitizer sanitize="False"/> + </param> + + <conditional name="paired"> + <param name="sPaired" type="select" label="Are you mapping paired-end reads?"> + <option value="paired">Paired-end</option> + <option value="single">Single-end</option> + </param> + <when value="single"> + <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)"> + <sanitizer sanitize="False"/> + </param> + </when> + <when value="paired"> + <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads"> + <sanitizer sanitize="False"/> + </param> + <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads"> + <sanitizer sanitize="False"/> + </param> + <param name="minlength" type="integer" value="200" label="Minimum insert size"/> + <param name="maxlength" type="integer" value="400" label="Maximum insert size"/> + </when> + </conditional> + + </inputs> + <outputs> + <data name="output1" format="samix" /> + <data name="output2" format="samix" > + <filter>paired['sPaired'] == "paired"</filter> + </data> + </outputs> + + <help> +This tool performs a NGS read mapping using rtg map + </help> + +</tool>