# HG changeset patch
# User jjalmagro
# Date 1422441951 18000
# Node ID 83b2fbc9368dc86883de0818ca742798356a6057
# Parent  7f4e7cdc5d33cb4fae5d1752d9bed9d901355fed
Uploaded

diff -r 7f4e7cdc5d33 -r 83b2fbc9368d findMotif.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findMotif.xml	Wed Jan 28 05:45:51 2015 -0500
@@ -0,0 +1,50 @@
+<tool id="find_motif" name="findMotif" version="1.0.0">
+  <description>Find specified motif in sequence</description>
+  <command>findMotif -motif="$motif" "$input1" 
+  #if str( $options_type.options_type_selector ) == "advanced":
+  -chr="${options_type.chr}" 
+  -strand="${options_type.strand} 
+  "${options_type.wigOutput}" 
+  #end if
+  > "$output"
+  </command>
+  <inputs>
+    <param format="fasta" name="input1" type="data" label="Sequences"/>
+    <param name="motif" type="text" value="acgt" size="17" />
+      
+      <conditional name="options_type">
+        <param name="options_type_selector" type="select" label="Options Configuration">
+          <option value="basic" selected="true">Basic</option>
+          <option value="advanced">Advanced</option>
+        </param>
+        <when value="basic">
+          <!-- do nothing here -->
+        </when>
+        <when value="advanced">
+      
+        <param name="chr" size="6" type="integer" value="1" label="Process only this chr from the sequence"/>
+	<param name="strand" type="select" label="Limit to only one strand">
+	  <option value="+">+</option>
+          <option value="-">-</option>
+	</param>
+	<param name="wigOutput" label="Output wiggle data format instead of bed file" type="boolean" truevalue="-wigOutput" falsevalue="" checked="False"/>
+        </when>
+      </conditional>
+  </inputs>
+  <outputs>
+    <data format="bed" name="output" label="${tool.name} on ${on_string} (bed)"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input1" value="find_motif_input.fa"/>
+      <output name="output" file="find_motif__output.bed"/>
+    </test>
+  </tests>
+
+  <help>
+Find specified motif in a sequence from a FASTA file.
+  </help>
+
+</tool>
+