diff galaxy-conf/PredictFAIRESignal.xml @ 12:81d5b81fb3c2 draft

Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/PredictFAIRESignal.xml	Wed Apr 25 16:53:48 2012 -0400
@@ -0,0 +1,42 @@
+<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.0.0">
+  <description>from nucleosome occupancy</description>
+  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.PredictFAIRESignal -i $input -s $sonication -c $crosslinking -x $extend -o $output</command>
+  <inputs>
+      <param format="bigwig,wig" name="input" type="data" label="Nucleosome occupancy data" />
+      <param format="tabular" name="sonication" type="data" label="Sonication fragment length distribution" />
+      <param name="crosslinking" type="float" value="1.0" label="Crosslinking coefficient" />
+      <param name="extend" type="integer" value="250" label="In silico read extension (bp)" />
+  </inputs>
+  <outputs>
+      <data format="wig" name="output" metadata_source="input" />
+  </outputs>
+  
+  <help>
+    
+This tool attempts to predict FAIRE signal from nucleosome occupancy by calculating the probability that a random sonicated fragment is occupied anywhere by a nucleosome.
+
+-----
+
+**Syntax**
+
+- **Nucleosome occupancy data** should be fragment coverage data from an MNase-seq experiment
+- **Sonication fragment length distribution:** The relative proportion of each size of fragment produced by sonication
+- **Crosslinking coefficient** is the efficiency of crosslinking (what fraction of the time is a nucleosome crosslinked)
+- **In silico read extension** is the length that single-end reads should be extended to match FAIRE-seq data
+
+-----
+
+Sonication fragment distribution must be provided in the following tabular format ::
+
+  length  proportion
+  
+So for example ::
+
+  1  0.1
+  2  0.2
+  3  0.3
+  4  0.2
+  5  0.2
+    
+  </help>
+</tool>