diff basecoverage.xml @ 0:1e6a9e97fa41

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/basecoverage.xml	Tue Apr 01 10:53:19 2014 -0400
@@ -0,0 +1,49 @@
+<tool id="gops_basecoverage_1" name="Base Coverage" version="0.0.1">
+  <description>of all intervals</description>
+  <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
+  <requirements>
+    <requirement type="package" version="0.7.1">bx-python</requirement>
+    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+  </requirements>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Compute coverage for</label>
+    </param>
+   </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </outputs>
+  <code file="operation_filter.py"/>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <output name="output" file="gops_basecoverage_out.txt" />     
+    </test>
+    <test>
+      <param name="input1" value="gops_bigint.interval" />
+      <output name="output" file="gops_basecoverage_out2.txt" />     
+    </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.
+
+This operation counts the total bases covered by a set of intervals.  Bases that are covered by more than one interval are **not** counted more than once towards the total.
+
+-----
+
+**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
+
+**Example**
+
+.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif
+
+
+</help>
+</tool>