# HG changeset patch
# User alenail
# Date 1459795934 14400
# Node ID 0eaa8225a09a718dea10a8c530e16e303213167d
# Parent  7a910b2c72ff92f5604d859dc7382a66390a7d35
Uploaded

diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/._map_to_known_genes.py
Binary file chipsequtil/._map_to_known_genes.py has changed
diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/._map_to_known_genes.xml
Binary file chipsequtil/._map_to_known_genes.xml has changed
diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/map_to_known_genes.py
--- a/chipsequtil/map_to_known_genes.py	Wed Mar 30 15:22:19 2016 -0400
+++ b/chipsequtil/map_to_known_genes.py	Mon Apr 04 14:52:14 2016 -0400
@@ -60,16 +60,6 @@
     gene_ref = parse_gene_ref(args[0])
     xref_fn = args[1]
     peaks_fn = args[2]
-    if opts.peaks_fmt == 'auto' :
-        path,ext = os.path.splitext(peaks_fn)
-        if ext.lower() == '.xls' :
-            opts.peaks_fmt = 'MACS'
-        elif ext.lower() == '.bed' :
-            opts.peaks_fmt = 'BED'
-        elif ext.lower() == '.narrowpeak' :
-            opts.peaks_fmt = 'BED'
-        else :
-            parser.error('Could not guess peaks file format by extension (%s), aborting'%ext)
 
     if opts.peaks_fmt == 'MACS' :
         peaks_reader_cls = MACSFile
diff -r 7a910b2c72ff -r 0eaa8225a09a chipsequtil/map_to_known_genes.xml
--- a/chipsequtil/map_to_known_genes.xml	Wed Mar 30 15:22:19 2016 -0400
+++ b/chipsequtil/map_to_known_genes.xml	Mon Apr 04 14:52:14 2016 -0400
@@ -31,12 +31,11 @@
     <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="auto">auto</option>
         <option value="MACS">MACS</option>
         <option selected="true" value="BED">BED</option>
     </param>
 
-    <param name="detail" checked="false" label="Add extra fields to output" type="boolean" truevalue="--detail" falsevalue="" help="" />
+    <param name="detail" checked="true" label="Add extra fields to output" 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>