# HG changeset patch
# User mvdbeek
# Date 1490557985 14400
# Node ID b07936a3962d17e92ce9d1a91d6f3fb329d09ae5
# Parent  e47f778202004ff413217d149d7b484450ebcf09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1

diff -r e47f77820200 -r b07936a3962d damidseq_core.xml
--- a/damidseq_core.xml	Sun Mar 26 10:31:55 2017 -0400
+++ b/damidseq_core.xml	Sun Mar 26 15:53:05 2017 -0400
@@ -5,8 +5,8 @@
     </requirements>
     <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ln -f -s '$dam' A001.fastq &&
         ln -f -s '$dam_fusion' A002.fastq &&
+        ln -f -s '$dam_only' A001.fastq &&
         ln -f -s '$index' index.txt &&
         HOME="\$PWD" damidseq_pipeline
         --bins=$bins
@@ -36,7 +36,7 @@
     </configfiles>
     <inputs>
         <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
-        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
+        <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
         <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
           <options from_data_table="bowtie2_indexes">
             <filter type="sort_by" column="2"/>
@@ -106,8 +106,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="dam" value="A001.fastq"/>
             <param name="dam_fusion" value="A002.fastq"/>
+            <param name="dam_only" value="A001.fastq"/>
             <param name="gatc_frag_file" value="dm6.GATC.gff"/>
             <param name="reference_index" value="dm6"/>
             <param name="norm_method" value="rpm"/>
diff -r e47f77820200 -r b07936a3962d index.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/index.html	Sun Mar 26 15:53:05 2017 -0400
@@ -0,0 +1,32 @@
+diff -r e47f77820200 damidseq_core.xml
+--- a/damidseq_core.xml	Sun Mar 26 10:31:55 2017 -0400
++++ b/damidseq_core.xml	Sun Mar 26 21:49:38 2017 +0200
+@@ -5,8 +5,8 @@
+     </requirements>
+     <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
+     <command detect_errors="aggressive"><![CDATA[
+-        ln -f -s '$dam' A001.fastq &&
+         ln -f -s '$dam_fusion' A002.fastq &&
++        ln -f -s '$dam_only' A001.fastq &&
+         ln -f -s '$index' index.txt &&
+         HOME="\$PWD" damidseq_pipeline
+         --bins=$bins
+@@ -36,7 +36,7 @@
+     </configfiles>
+     <inputs>
+         <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
+-        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
++        <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
+         <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+           <options from_data_table="bowtie2_indexes">
+             <filter type="sort_by" column="2"/>
+@@ -106,8 +106,8 @@
+     </outputs>
+     <tests>
+         <test>
+-            <param name="dam" value="A001.fastq"/>
+             <param name="dam_fusion" value="A002.fastq"/>
++            <param name="dam_only" value="A001.fastq"/>
+             <param name="gatc_frag_file" value="dm6.GATC.gff"/>
+             <param name="reference_index" value="dm6"/>
+             <param name="norm_method" value="rpm"/>
diff -r e47f77820200 -r b07936a3962d patch
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/patch	Sun Mar 26 15:53:05 2017 -0400
@@ -0,0 +1,32 @@
+diff -r e47f77820200 damidseq_core.xml
+--- a/damidseq_core.xml	Sun Mar 26 10:31:55 2017 -0400
++++ b/damidseq_core.xml	Sun Mar 26 21:49:38 2017 +0200
+@@ -5,8 +5,8 @@
+     </requirements>
+     <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
+     <command detect_errors="aggressive"><![CDATA[
+-        ln -f -s '$dam' A001.fastq &&
+         ln -f -s '$dam_fusion' A002.fastq &&
++        ln -f -s '$dam_only' A001.fastq &&
+         ln -f -s '$index' index.txt &&
+         HOME="\$PWD" damidseq_pipeline
+         --bins=$bins
+@@ -36,7 +36,7 @@
+     </configfiles>
+     <inputs>
+         <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
+-        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
++        <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
+         <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+           <options from_data_table="bowtie2_indexes">
+             <filter type="sort_by" column="2"/>
+@@ -106,8 +106,8 @@
+     </outputs>
+     <tests>
+         <test>
+-            <param name="dam" value="A001.fastq"/>
+             <param name="dam_fusion" value="A002.fastq"/>
++            <param name="dam_only" value="A001.fastq"/>
+             <param name="gatc_frag_file" value="dm6.GATC.gff"/>
+             <param name="reference_index" value="dm6"/>
+             <param name="norm_method" value="rpm"/>