diff merge.xml @ 0:b488a1fa07f6

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.xml	Tue Apr 01 10:53:37 2014 -0400
@@ -0,0 +1,62 @@
+<tool id="gops_merge_1" name="Merge">
+  <description>the overlapping intervals of a dataset</description>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+  </requirements>
+  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Merge overlaping regions of</label>
+    </param>
+    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
+      <label>Output 3 column bed</label>
+    </param>
+   </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py">
+    <hook exec_after_process="exec_after_merge" />
+  </code>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <output name="output" file="gops-merge.dat" />
+      <param name="returntype" value="true" />
+    </test>
+    <test>
+      <param name="input1" value="2_mod.bed" ftype="interval"/>
+      <output name="output" file="gops_merge_diffCols.dat" />
+      <param name="returntype" value="true" />
+    </test>
+    <test>
+      <param name="input1" value="gops_bigint.interval" />
+      <output name="output" file="gops_merge_out2.bed" />
+      <param name="returntype" value="true" />
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
+
+-----
+
+**Screencasts!**
+
+See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
+
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
+
+-----
+
+This operation merges all overlapping intervals into single intervals.
+
+**Example**
+
+.. image:: ${static_path}/operation_icons/gops_merge.gif
+
+</help>
+</tool>
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