# HG changeset patch
# User mvdbeek
# Date 1490280941 14400
# Node ID 0d1514ecd757eae1651d186533edb60cd2403340
# Parent  eb3a145c4962604ac45f46106c35da4c95870253
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit e6582f259ba7d57bc559887a87ee56e6d29f942e

diff -r eb3a145c4962 -r 0d1514ecd757 damidseq_core.xml
--- a/damidseq_core.xml	Wed Mar 22 09:56:09 2017 -0400
+++ b/damidseq_core.xml	Thu Mar 23 10:55:41 2017 -0400
@@ -1,15 +1,14 @@
-<tool id="damidseq_core" name="damidseq" version="0.1.0">
-    <description>align, extend and normalize a DAMID-seq experiment</description>
+<tool id="damidseq_core" name="damidseq" version="0.1.1">
+    <description>align, extend and normalize a DamID-seq experiment</description>
     <requirements>
         <requirement type="package" version="1.4">damidseq_pipeline</requirement>
     </requirements>
     <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
-        export HOME="\$PWD" &&
-        ln -f -s '$dam' A001.$dam.ext &&
-        ln -f -s '$dam_fusion' A002.$dam_fusion.ext &&
+        ln -f -s '$dam' A001.fastq &&
+        ln -f -s '$dam_fusion' A002.fastq &&
         ln -f -s '$index' index.txt &&
-        damidseq_pipeline
+        HOME="\$PWD" damidseq_pipeline
         --bins=$bins
         --bowtie=1
         --bowtie2_genome_dir='$reference_index.fields.path'
@@ -28,16 +27,16 @@
         --qscore1max=$qscore1max
         --qscore1min=$qscore1min
         --qscore2max=$qscore2max
-        --threads=\${GALAXY_SLOTS:-4} &&
-        mv Fusion-vs-Dam.*.$output_format fusion.output
+        --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
+        mv Fusion-vs-Dam.* fusion.output
     ]]></command>
     <configfiles>
         <configfile name="index">A1	Dam
 A2	Fusion</configfile>
     </configfiles>
     <inputs>
-        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control DAM alignment file"/>
-        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion alignment file"/>
+        <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
+        <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion 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"/>
@@ -46,7 +45,7 @@
         </param>
         <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
         <param name="output_format" type="select" label="Select the output format for the peaks">
-            <option value="bedgraph">Bedgraph</option>
+            <option value="bedgraph">Bed</option>
             <option value="gff">GFF</option>
         </param>
         <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
@@ -71,22 +70,48 @@
         <param argument="--qscore2max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from fusion-protein array"/>
     </inputs>
     <outputs>
-        <data name="output_ratio" format="bedgraph" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio">
+        <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio">
             <change_format>
                 <when input="output_format" value="gff" format="gff" />
             </change_format>
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="reference_index" column="0"/>
+                    </option>
+                </action>
+            </actions>
         </data>
-        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment"/>
-        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment"/>
+        <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment">
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="reference_index" column="0"/>
+                    </option>
+                </action>
+            </actions>
+        </data>
+        <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment">
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="reference_index" column="0"/>
+                    </option>
+                </action>
+            </actions>
+        </data>
     </outputs>
     <tests>
         <test>
             <param name="dam" value="A001.fastq"/>
             <param name="dam_fusion" value="A002.fastq"/>
             <param name="gatc_frag_file" value="dm6.GATC.gff"/>
-            <param name="index" value="dm6"/>
+            <param name="reference_index" value="dm6"/>
             <param name="norm_method" value="rpm"/>
-            <output name="output_ratio" file="output_ratio.bedgraph"/>
+            <output name="output_ratio" file="output_ratio.bed"/>
             <output name="control_output" file="control.bam"/>
             <output name="fusion_output" file="fusion.bam"/>
         </test>
diff -r eb3a145c4962 -r 0d1514ecd757 test-data/bt2/.GATC.gff
--- a/test-data/bt2/.GATC.gff	Wed Mar 22 09:56:09 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-X	.	.	157	161	1	+	.	.
-X	.	.	364	368	1	+	.	.
-X	.	.	499	503	1	+	.	.
diff -r eb3a145c4962 -r 0d1514ecd757 test-data/output_ratio.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_ratio.bed	Thu Mar 23 10:55:41 2017 -0400
@@ -0,0 +1,3 @@
+track type=bedGraph name="Fusion-vs-Dam" description="Fusion DamIDseq"
+X	159	366	0
+X	366	501	0
diff -r eb3a145c4962 -r 0d1514ecd757 test-data/output_ratio.bedgraph
--- a/test-data/output_ratio.bedgraph	Wed Mar 22 09:56:09 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-track type=bedGraph name="Fusion-vs-Dam" description="Fusion DamIDseq"
-X	159	366	0
-X	366	501	0