# HG changeset patch
# User iuc
# Date 1528363282 14400
# Node ID c97a786e8fb5df7780b61d641ad82ec508b63213
# Parent  1de83981d43cccd6802855d719f0f99c261dbf31
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 1fe103338548dd65731a5a0887be59745370debd

diff -r 1de83981d43c -r c97a786e8fb5 diffbind.xml
--- a/diffbind.xml	Wed May 30 12:25:42 2018 -0400
+++ b/diffbind.xml	Thu Jun 07 05:21:22 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="diffbind" name="DiffBind" version="2.6.6.3">
+<tool id="diffbind" name="DiffBind" version="2.6.6.4">
     <description> differential binding analysis of ChIP-Seq peak data</description>
     <requirements>
         <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>
@@ -37,16 +37,18 @@
     #set $bam_controls = list()
 
     #for $file in $g.peaks:
-        #set $file_name = re.sub('[^\w\-\s]', '_', str($file.element_identifier))
-        ln -s '${file}' ${g.groupName}-${file_name}-peaks.bed &&
-        $peak_files.append(str($g.groupName) + '-' + $file_name + '-peaks.bed')
+        #set $file_name = str($g.groupName) + "-" + re.sub('[^\w\-]', '_', str($file.element_identifier)) + "-peaks.bed"
+        ln -s '${file}' '${file_name}' &&
+        $peak_files.append($file_name)
     #end for
 
     #for $bam in $g.bamreads:
-        #set $bam_name = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
-        ln -s '${bam}' ${bam_name}-bamreads.bam &&
-        ln -s ${bam.metadata.bam_index} ${bam_name}-bamreads.bai &&
-        $bam_files.append($bam_name + '-bamreads.bam')
+        #set $bam_name = re.sub('[^\w\-]', '_', str($bam.element_identifier))
+        #set $bam_file = $bam_name + "-bamreads.bam"
+        #set $bam_index = $bam_name + "-bamreads.bai"
+        ln -s '${bam}' '${bam_file}' &&
+        ln -s '${bam.metadata.bam_index}' '${bam_index}' &&
+        $bam_files.append($bam_file)
     #end for
 
     $temp_factor.append( {str($g.groupName): $peak_files} )
@@ -54,10 +56,14 @@
 
     #if str( $g.bamcontrol ) != 'None':
         #for $ctrl in $g.bamcontrol:
-            #set $ctrl_name = re.sub('[^\w\-\s]', '_', str($ctrl.element_identifier))
-            ln -s '${ctrl}' ${g.groupName}-${ctrl_name}-bamcontrol.bam &&
-            ln -s ${ctrl.metadata.bam_index} ${g.groupName}-${ctrl_name}-bamcontrol.bai &&
-            $bam_controls.append(str($g.groupName) + '-' + $ctrl_name + '-bamcontrol.bam')
+            #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
+            #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
+            #set ctrl_index = $ctrl_name + "-bamcontrol.bai"
+            #if $ctrl_file not in json.dumps($temp_factor):
+                ln -s '${ctrl}' '${ctrl_file}' &&
+                ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
+            #end if
+            $bam_controls.append($ctrl_file)
         #end for
         $temp_factor.append( {str($g.groupName): $bam_controls} )
     #end if
@@ -113,8 +119,8 @@
                 <validator type="empty_field" />
             </param>
             <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
-            <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used in the Peak calling."/>
-            <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one, see Help section below."/>
+            <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
+            <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
         </repeat>
 
         <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">
@@ -204,6 +210,24 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Ensure control BAMs input works -->
+        <test expect_num_outputs="1">
+            <repeat name="rep_group">
+                <param name="groupName" value="Resistant"/>
+                <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
+                <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
+                <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
+            </repeat>
+            <repeat name="rep_group">
+                <param name="groupName" value="Responsive"/>
+                <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
+                <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
+                <param name="bamcontrol" ftype="bam" value="input1.bam,input2.bam" />
+            </repeat>
+            <param name="scorecol" value="5" />
+            <param name="format" value="interval"/>
+            <output name="outfile" ftype="interval" value="out_diffbind_ctrl.interval" />
+        </test>
         <!-- Ensure BED output works -->
         <test expect_num_outputs="1">
             <repeat name="rep_group">
@@ -266,7 +290,7 @@
 as well as comparing the results of an occupancy-based analysis with an affinity-based one.
 Finally, certain technical aspects of the how these analyses are accomplished are detailed.
 
-Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).
+**Note this DiffBind tool requires a minimum of four samples (two groups with two replicates each).**
 
 -----
 
diff -r 1de83981d43c -r c97a786e8fb5 test-data/input1.bam
Binary file test-data/input1.bam has changed
diff -r 1de83981d43c -r c97a786e8fb5 test-data/input2.bam
Binary file test-data/input2.bam has changed
diff -r 1de83981d43c -r c97a786e8fb5 test-data/out_diffbind_ctrl.interval
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out_diffbind_ctrl.interval	Thu Jun 07 05:21:22 2018 -0400
@@ -0,0 +1,6 @@
+Chrom	Start	End	Name	Score	Strand	Comment
+chr18	394599	396513	DiffBind	0	.	1914|6.86|3.93|7.76|-3.83|2.05e-37|2.85e-34
+chr18	399013	400382	DiffBind	0	.	1369|7.47|6.71|7.96|-1.25|2.31e-09|1.61e-06
+chr18	346463	347342	DiffBind	0	.	879|4.18|5.16|-0.93|6.09|1.1e-07|5.13e-05
+chr18	111566	112005	DiffBind	0	.	439|5.55|6.41|3.03|3.38|5.03e-06|0.00175
+chr18	371109	372102	DiffBind	0	.	993|4.04|-0.02|5|-5.02|1.23e-05|0.00344