Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/mapx.xml @ 1:8593828f91e7 default tip
Full galaxy wrapper
| author | diego |
|---|---|
| date | Sat, 21 Apr 2012 21:36:15 -0400 |
| parents | |
| children |
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| 0:d50638ebd809 | 1:8593828f91e7 |
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| 1 <tool id="rtg_mapx" name="MapX"> | |
| 2 <description>protein reads with rtg mapx</description> | |
| 3 <command interpreter="bash">galaxy-rtg-mapx-wrapper.sh $output1 $__new_file_path__ | |
| 4 mapx -t ${template.extra_files_path} | |
| 5 --repeat-freq ${repeat} | |
| 6 -i ${reads.extra_files_path} | |
| 7 --max-alignment-score $maxscore | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/> | |
| 11 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/> | |
| 12 <param name="repeat" type="text" value="90%" label="Repeat frequency"> | |
| 13 <sanitizer sanitize="False"/> | |
| 14 </param> | |
| 15 | |
| 16 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)"> | |
| 17 <sanitizer sanitize="False"/> | |
| 18 </param> | |
| 19 | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="output1" format="tabular" /> | |
| 23 </outputs> | |
| 24 | |
| 25 <help> | |
| 26 This tool performs a NGS protein read mapping using rtg mapx | |
| 27 </help> | |
| 28 | |
| 29 </tool> |