Mercurial > repos > jeremyjliu > region_motif_enrichment
comparison region_motif_compare.xml @ 0:5c044273554d draft
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| author | jeremyjliu |
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| date | Tue, 05 Aug 2014 13:56:22 -0400 |
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| -1:000000000000 | 0:5c044273554d |
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| 1 <tool id="region_motif_compare" name="Region Motif Count Compare"> | |
| 2 <description>for comparing the motif counts in different region sets</description> | |
| 3 <command interpreter="bash"> | |
| 4 /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/tools/my_tools/region_motif_compare.r --args $GALAXY_ROOT_DIR $db_type $in_tab_1 $in_tab_2 $out_enriched $out_depleted $out_plots | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param name="in_tab_1" type="data" format="tabular" label="Region Set 1 Motif Count File"/> | |
| 8 <param name="in_tab_2" type="data" format="tabular" label="Region Set 2 Motif Count File"/> | |
| 9 <param name="db_type" type="select" label="Select Motif Database" > | |
| 10 <option value="t">Test Pouya Subset (hg19)</option> | |
| 11 <option value="p">Pouya Encode Motifs (hg19)</option> | |
| 12 <option value="j">Jaspar and Jolma Motifs (hg19)</option> | |
| 13 <option value="m">Mouse Motifs (mm9)</option> | |
| 14 <option value="c">Pouya, Jaspar, and Jolma Combined (hg19)</option> | |
| 15 </param> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="out_enriched" format="tabular" label="Enriched Motifs"/> | |
| 19 <data name="out_depleted" format="tabular" label="Depleted Motifs"/> | |
| 20 <data name="out_plots" format="png" label="Motif Count Comparison Plots"/> | |
| 21 </outputs> | |
| 22 | |
| 23 <help> | |
| 24 This tools reads in two counts file and determines enriched and depleted | |
| 25 motifs in two different region sets based on poisson calculation with | |
| 26 gc correction. | |
| 27 </help> | |
| 28 | |
| 29 </tool> |