diff region_motif_intersect.xml @ 30:da0bc6dead0d draft

Restore deleted source files

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+++ b/region_motif_intersect.xml	Mon Jan 05 22:28:37 2015 -0500
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+<tool id="region_motif_intersect" name="Region Motif Intersect">
+  <description>for computing the motifs that lie inside a region set</description>
+  <requirements>
+    <requirement type="set_environment">RMOTIF_PATH</requirement>
+    <requirement type="package" version="1.0.0">MOTIFS</requirement>
+  </requirements>
+  <command interpreter="Rscript">
+    region_motif_intersect.r --args \$RMOTIF_PATH $db_type $in_bed $out_tab
+  </command>
+  <inputs>
+    <param name="in_bed" type="data" format="bed" label="Input BED File" />
+    <param name="db_type" type="select" label="Select Motif Database" >
+      <option value="t">Test Pouya Subset (hg19)</option>
+      <option value="p">Pouya Encode Motifs (hg19)</option>
+      <option value="j">Jaspar and Jolma Motifs (hg19)</option>
+      <option value="m">Mouse Motifs (mm9)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_tab" format="tabular" />
+  </outputs>
+
+  <help>
+    This tool computes the motifs and the number of motifs that intersect
+    any region in a input set of regions.
+  </help>
+ 
+</tool>
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