Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/PredictFAIRESignal.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
children
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--- a/galaxy-conf/PredictFAIRESignal.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/PredictFAIRESignal.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -1,11 +1,11 @@
-<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.0.0">
+<tool id="PredictFAIRE" name="Predict FAIRE signal" version="1.1.0">
   <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)" />
+      <param name="extend" type="integer" value="250" label="In silico read extension (-1 for paired-end mode)" />
   </inputs>
   <outputs>
       <data format="wig" name="output" metadata_source="input" />