diff tools/new_operations/complement.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/complement.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,61 @@
+<tool id="gops_complement_1" name="Complement">
+  <description>intervals of a dataset</description>
+  <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Complement regions of</label>
+    </param>
+    <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
+    </param>
+   </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py"/>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" dbkey="?" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out.bed" />
+    </test>
+    <test>
+      <param name="input1" value="2_mod.bed" ftype="interval" dbkey="?" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out_diffCols.dat" />
+    </test>
+    <test>
+      <param name="input1" value="gops_bigint.interval" dbkey="?" />
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out2.bed" />
+    </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 complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input interval.
+
+-----
+
+**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
+
+-----
+
+**Syntax**
+
+- **Genome-wide complement** will complement all chromosomes of the genome.  Leaving this option unchecked will only complement chromosomes present in the dataset.
+
+-----
+
+**Example**
+
+.. image:: ./static/operation_icons/gops_complement.gif
+
+</help>
+</tool>