# HG changeset patch
# User iuc
# Date 1566073444 14400
# Node ID db50f51a29529fc5c38e2bac9a4d82f0b1020c49
# Parent  a41d96fc0b2013b1bd02b3afd83b3b41a74f792d
"planemo upload for repository https://github.com/jsh58/Genrich commit 85e0bb6eaeaf1b82357cb95abf6ebad6dd4ab492"

diff -r a41d96fc0b20 -r db50f51a2952 genrich.xml
--- a/genrich.xml	Mon Jul 15 09:43:27 2019 -0400
+++ b/genrich.xml	Sat Aug 17 16:24:04 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="genrich" name="Genrich" version="0.5">
+<tool id="genrich" name="Genrich" version="0.5+galaxy1">
     <description>Detecting sites of genomic enrichment</description>
     <requirements>
         <requirement type="package" version="0.5">genrich</requirement>
@@ -38,7 +38,7 @@
 ####################
 
 #if $filter_options.duplicates:
-    '$filter_options.duplicates' '${out_dups}'
+    -r -R '${out_dups}'
 #end if
 
 #if $filter_options.exclude_chr:
@@ -118,10 +118,13 @@
                 <option value="Yes">Yes</option>
             </param>
             <when value="No" >
-                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File(s)" />
+                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" label="Treatment File"
+                    help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
             </when>
             <when value="Yes">
-                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true" label="Treatment Files" />
+                <param name="input_treatment_file" argument="-t" type="data" format="qname_sorted.bam" multiple="true"
+                    label="Treatment Files."
+                    help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
             </when>
         </conditional>
 
@@ -137,10 +140,12 @@
                         <option value="Yes">Yes</option>
                     </param>
                     <when value="No" >
-                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File(s)" />
+                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" label="Control File"
+                            help="This file should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
                     </when>
                     <when value="Yes">
-                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files" />
+                        <param name="input_control_file" argument="-c" type="data" format="qname_sorted.bam" multiple="true" label="Control Files"
+                            help="These files should be a name-sorted BAM file. 'samtools sort' can do this with the 'name (-n)' parameter." />
                     </when>
                 </conditional>
             </when>