Mercurial > repos > diego > rtg_investigator
view tools/rtg/cgmap.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_cgmap" name="CG map"> <description>reads with rtg cg map</description> <command interpreter="bash">galaxy-rtg-map-wrapper.sh paired $output1 $output2 $__new_file_path__ cgmap -t ${template.extra_files_path} --repeat-freq ${repeat} -i ${reads.extra_files_path} --min-insert-size $minlength --max-insert-size $maxlength --max-mated-score $maxscore --max-unmated-score $maxuscore </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> <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="0" label="Minimum insert size"/> <param name="maxlength" type="integer" value="1000" label="Maximum insert size"/> </inputs> <outputs> <data name="output1" format="samix" label="Cgmap mated on reads data ${reads.hid} and template data ${template.hid}"/> <data name="output2" format="samix" label="Cgmap unmated on reads data ${reads.hid} and template data ${template.hid}"/> </outputs> <help> This tool performs a NGS read mapping using rtg cgmap </help> </tool>