# HG changeset patch
# User cmmt
# Date 1327314291 18000
# Node ID 4c9201237641dab077afe732ba8a6325463e7c0f
# Parent  519e45d9539fcedc2bde31196e474b77b6c04319
Uploaded

diff -r 519e45d9539f -r 4c9201237641 chromatral.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromatral.xml	Mon Jan 23 05:24:51 2012 -0500
@@ -0,0 +1,60 @@
+<tool id="chromatra_l" name="Chromatra L" version="1.0.0">
+  <description>for visualizing genome-wide chromatin modifications</description>
+  <command interpreter="python">chromatral.py $gffinput $feainput $imgformat $stepwidth $upstreamstretch $maxx $tickspacing '$title' $output</command>
+  <inputs>
+    <param name="gffinput" format="gff" type="data" label="Normalized enrichment scores"/>
+    <param name="feainput" format="tabular" type="data" label="Feature descriptions"/>
+    <param name="imgformat" type="select" label="Image format">
+        <option value="svg" selected="true">svg</option>
+        <option value="png">png</option>
+	<option value="pdf">pdf</option>
+    </param>
+    <param name="stepwidth" type="integer" value="150" min="1" label="Bin size in bp" />
+    <param name="upstreamstretch" type="integer" value="450" min="0" label="Number of bp upstream of feature start to be plotted" />
+    <param name="maxx" type="integer" value="5000" label="Max bp to be plotted  along x-coordinate. (Enter -1 for max feature length)"/>
+    <param name="tickspacing" type="integer" value="1000" label="Tick spacing along x-coordinate" />
+    <param name="title" type="text" value="" size="30" label="Plot title" />
+  </inputs>
+  <outputs>
+    <data format="svg" name="output">
+	<change_format>
+		<when input="imgformat" value="png" format="png" />
+		<when input="imgformat" value="pdf" format="pdf" />
+		<when input="imgformat" value="svg" format="svg" />
+	</change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="python-module">matplotlib</requirement>
+  </requirements>
+
+  <help>
+CHROMATRA L visualizes the enrichment of chromatin modification across genomic features (e.g. all transcripts of a genome) in an unbiased way by accounting for feature length.
+
+-----
+
+.. class:: infomark
+
+**Normalized enrichment scores**
+
+Enrichment scores must be provided in *GGFv3* format.
+
+.. class:: infomark
+
+**Feature descriptions**
+
+Features must be provided in a *TAB*-delimited format in this order:
+
+-1. feature name
+
+-2. chromosome number
+
+-3. strand
+
+-4. feature start
+
+-5. feature end
+  </help>
+
+</tool>