# HG changeset patch
# User alenail
# Date 1459796211 14400
# Node ID 124231ed24023ab2ccf0b59e6f0e1cb763ef3b24
# Parent  199989365def5e99db5cd7789f3e07ab15a29cdb
Uploaded

diff -r 199989365def -r 124231ed2402 chipsequtil/._map_to_known_genes.py
Binary file chipsequtil/._map_to_known_genes.py has changed
diff -r 199989365def -r 124231ed2402 chipsequtil/._map_to_known_genes.xml
Binary file chipsequtil/._map_to_known_genes.xml has changed
diff -r 199989365def -r 124231ed2402 chipsequtil/map_to_known_genes.xml
--- a/chipsequtil/map_to_known_genes.xml	Mon Apr 04 14:52:25 2016 -0400
+++ b/chipsequtil/map_to_known_genes.xml	Mon Apr 04 14:56:51 2016 -0400
@@ -28,14 +28,14 @@
     <param name="upst_win" type="integer" label="Upstream Window" help="Window width in base pairs to consider promoter region [default: %default]" optional="false" value="5500" />
     <param name="dnst_win" type="integer" label="Downstream Window" help="Window width in base pairs to consider downstream region [default: %default]" optional="false" value="2500" />
 
-    <param name="tss" checked="true" label="calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" />
+    <param name="tss" checked="true" label="Calculate downstream window from transcription start site instead of transcription end site" type="boolean" truevalue="--tss" falsevalue="" help="" />
 
     <param name="peaks_fmt" type="select" label="Peaks Format" help="Format of peaks input file" optional="false">
         <option value="MACS">MACS</option>
         <option selected="true" value="BED">BED</option>
     </param>
 
-    <param name="detail" checked="true" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" />
+    <param name="detail" checked="true" label="Append the following fields to each row: peak loc, dist from feature, map type, map subtype" type="boolean" truevalue="--detail" falsevalue="" help="" />
     <param name="intergenic" checked="false" label="Write intergenic peaks to the gene file as well with None as gene ID" type="boolean" truevalue="--intergenic" falsevalue="" help="" />
   </inputs>
   <outputs>
diff -r 199989365def -r 124231ed2402 chipsequtil/tool_dependencies.xml
--- a/chipsequtil/tool_dependencies.xml	Mon Apr 04 14:52:25 2016 -0400
+++ b/chipsequtil/tool_dependencies.xml	Mon Apr 04 14:56:51 2016 -0400
@@ -3,7 +3,7 @@
     <package name="chipsequtil" version="1.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://github.com/adamlabadorf/chipsequtil/archive/master.zip</action>
+                <action type="download_by_url">https://github.com/fraenkel-lab/chipsequtil/archive/master.zip</action>
                 <action type="shell_command">cp org_settings.cfg src/chipsequtil/</action>
                 <action type="shell_command">python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                 <action type="set_environment">