# HG changeset patch
# User mvdbeek
# Date 1524078162 14400
# Node ID 6c00620084a5d4d4803d357998a54beec9922bf4
# Parent  b07936a3962d17e92ce9d1a91d6f3fb329d09ae5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 3b71bf884857aa89f39849a6c64c7f6d8d97c2d1

diff -r b07936a3962d -r 6c00620084a5 damidseq_core.xml
--- a/damidseq_core.xml	Sun Mar 26 15:53:05 2017 -0400
+++ b/damidseq_core.xml	Wed Apr 18 15:02:42 2018 -0400
@@ -5,8 +5,10 @@
     </requirements>
     <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ln -f -s '$dam_fusion' A002.fastq &&
-        ln -f -s '$dam_only' A001.fastq &&
+        #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq'
+        #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq'
+        ln -f -s '$dam' $dam_file &&
+        ln -f -s '$dam_fusion' $dam_fusion_file &&
         ln -f -s '$index' index.txt &&
         HOME="\$PWD" damidseq_pipeline
         --bins=$bins
@@ -36,7 +38,7 @@
     </configfiles>
     <inputs>
         <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
-        <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
+        <param argument="--dam" 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 +108,18 @@
     </outputs>
     <tests>
         <test>
+            <param name="dam" value="A001.fastq.gz"/>
+            <param name="dam_fusion" value="A002.fastq.gz"/>
+            <param name="gatc_frag_file" value="dm6.GATC.gff"/>
+            <param name="reference_index" value="dm6"/>
+            <param name="norm_method" value="rpm"/>
+            <output name="output_ratio" file="output_ratio.bed"/>
+            <output name="control_output" file="control.bam"/>
+            <output name="fusion_output" file="fusion.bam"/>
+        </test>
+        <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 b07936a3962d -r 6c00620084a5 index.html
--- a/index.html	Sun Mar 26 15:53:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-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 b07936a3962d -r 6c00620084a5 patch
--- a/patch	Sun Mar 26 15:53:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-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 b07936a3962d -r 6c00620084a5 test-data/A001.fastq.gz
Binary file test-data/A001.fastq.gz has changed
diff -r b07936a3962d -r 6c00620084a5 test-data/A002.fastq.gz
Binary file test-data/A002.fastq.gz has changed