diff cluster.xml @ 0:45fb880ab3bf

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.xml	Tue Apr 01 09:12:53 2014 -0400
@@ -0,0 +1,100 @@
+<tool id="gops_cluster_1" name="Cluster" version="0.0.1">
+  <description>the 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>
+  <trackster_conf/>
+  <command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command>
+  <inputs>
+    <param format="interval" name="input1" type="data">
+      <label>Cluster intervals of</label>
+    </param>
+    <param name="distance" size="5" type="integer" value="1" help="(bp)">
+      <label>max distance between intervals</label>
+    </param>
+    <param name="minregions" size="5" type="integer" value="2">
+      <label>min number of intervals per cluster</label>
+    </param>
+	<param name="returntype" type="select" label="Return type">
+		<option value="1">Merge clusters into single intervals</option>
+		<option value="2">Find cluster intervals; preserve comments and order</option>
+		<option value="3">Find cluster intervals; output grouped by clusters</option>
+		<option value="4">Find the smallest interval in each cluster</option>
+		<option value="5">Find the largest interval in each cluster</option>
+	</param>
+   </inputs>
+  <outputs>
+    <data format="input" name="output" metadata_source="input1" />
+  </outputs>
+  <code file="operation_filter.py">
+    <hook exec_after_process="exec_after_cluster" />
+  </code>
+  <tests>
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="1" />
+      <output name="output" file="gops-cluster-1.bed" />     
+    </test>
+    <test>
+      <param name="input1" value="gops_cluster_bigint.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="1" />
+      <output name="output" file="gops-cluster-1.bed" />     
+    </test>
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="2" />
+      <output name="output" file="gops-cluster-2.bed" />     
+    </test>    
+    <test>
+      <param name="input1" value="5.bed" />
+      <param name="distance" value="1" />
+      <param name="minregions" value="2" />
+      <param name="returntype" value="3" />
+      <output name="output" file="gops-cluster-3.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.
+
+-----
+
+**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**
+
+- **Maximum distance** is greatest distance in base pairs allowed between intervals that will be considered &quot;clustered&quot;.  **Negative** values for distance are allowed, and are useful for clustering intervals that overlap.
+- **Minimum intervals per cluster** allow a threshold to be set on the minimum number of intervals to be considered a cluster.  Any area with less than this minimum will not be included in the output.
+- **Merge clusters into single intervals** outputs intervals that span the entire cluster.
+- **Find cluster intervals; preserve comments and order** filters out non-cluster intervals while maintaining the original ordering and comments in the file.
+- **Find cluster intervals; output grouped by clusters** filters out non-cluster intervals, but outputs the cluster intervals so that they are grouped together. Comments and original ordering in the file are lost.
+
+-----
+
+**Examples**
+
+Find Clusters:
+
+.. image:: ${static_path}/operation_icons/gops_clusterFind.gif
+
+Merge Clusters:
+
+.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif
+
+</help>
+</tool>