Mercurial > repos > jeremyjliu > region_motif_enrichment
comparison region_motif_intersect.xml @ 6:d281fed8ec61 draft
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author | jeremyjliu |
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date | Sat, 25 Oct 2014 15:07:28 -0400 |
parents | 5d9014614d28 |
children | 0c1627c2f09d |
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5:7a3bb055f3d0 | 6:d281fed8ec61 |
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1 <tool id="region_motif_intersect" name="Region Motif Intersect"> | 1 <tool id="region_motif_intersect" name="Region Motif Intersect"> |
2 <description>for computing the motifs that lie inside a region set</description> | 2 <description>for computing the motifs that lie inside a region set</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="set_environment">MOTIF_DB_PATH</requirement> | 4 <requirement type="set_environment">R_SCRIPT_PATH</requirement> |
5 <requirement type="package" version="2.15.1">R</requirement> | |
5 </requirements> | 6 </requirements> |
6 <command interpreter="Rscript"> | 7 <command interpreter="Rscript"> |
7 region_motif_intersect.r --args $MOTIF_DB_PATH $db_type $in_bed $out_tab | 8 region_motif_intersect.r --args \$R_SCRIPT_PATH $db_type $in_bed $out_tab |
8 </command> | 9 </command> |
9 <inputs> | 10 <inputs> |
10 <param name="in_bed" type="data" format="bed" label="Input BED File" /> | 11 <param name="in_bed" type="data" format="bed" label="Input BED File" /> |
11 <param name="db_type" type="select" label="Select Motif Database" > | 12 <param name="db_type" type="select" label="Select Motif Database" > |
12 <option value="t">Test Pouya Subset (hg19)</option> | 13 <option value="t">Test Pouya Subset (hg19)</option> |