annotate region-motif-compare/region_motif_intersect.xml @ 17:7afdfd4f4c1b draft

Uploaded
author jeremyjliu
date Wed, 12 Nov 2014 15:21:11 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
1 <tool id="region_motif_intersect" name="Region Motif Intersect">
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
2 <description>for computing the motifs that lie inside a region set</description>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
3 <requirements>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
4 <requirement type="set_environment">RMOTIF_PATH</requirement>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
5 </requirements>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
6 <command interpreter="Rscript">
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
7 region_motif_intersect.r --args \$RMOTIF_PATH $db_type $in_bed $out_tab
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
8 </command>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
9 <inputs>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
10 <param name="in_bed" type="data" format="bed" label="Input BED File" />
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
11 <param name="db_type" type="select" label="Select Motif Database" >
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
12 <option value="t">Test Pouya Subset (hg19)</option>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
13 <option value="p">Pouya Encode Motifs (hg19)</option>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
14 <option value="j">Jaspar and Jolma Motifs (hg19)</option>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
15 <option value="m">Mouse Motifs (mm9)</option>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
16 </param>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
17 </inputs>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
18 <outputs>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
19 <data name="out_tab" format="tabular" />
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
20 </outputs>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
21
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
22 <help>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
23 This tool computes the motifs and the number of motifs that intersect
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
24 any region in a input set of regions.
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
25 </help>
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
26
7afdfd4f4c1b Uploaded
jeremyjliu
parents:
diff changeset
27 </tool>