# HG changeset patch
# User crs4
# Date 1426603473 14400
# Node ID d5464c9e1723f64e1c94391d63e90038ffb2106c
# Parent  ddcbf8732706e46e3774201dd61bfe76b21ea9fb
Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).

diff -r ddcbf8732706 -r d5464c9e1723 edge_pro.xml
--- a/edge_pro.xml	Mon Jan 19 12:48:51 2015 -0500
+++ b/edge_pro.xml	Tue Mar 17 10:44:33 2015 -0400
@@ -10,11 +10,18 @@
     -g $genome
     -p $ptt
     -r $rnt
-    ## First input file always required
-    -u $singlePaired.input1
-    ## Second input only if input is paired-end
-    #if $singlePaired.sPaired == "paired"
+
+    #if $singlePaired.sPaired == "single"
+      -u $singlePaired.input1
+    #else if $singlePaired.sPaired == "paired"
+      -u $singlePaired.input1
       -v $singlePaired.input2
+    #else if $singlePaired.sPaired == "pairedCollection"
+      -u $singlePaired.input.forward
+      -v $singlePaired.input.reverse
+    #end if
+
+    #if $singlePaired.sPaired in ["paired", "pairedCollection"]
       #if str($singlePaired.minInsertSize)
         -m $singlePaired.minInsertSize
       #end if
@@ -52,6 +59,7 @@
       <param name="sPaired" type="select" label="Is this library mate-paired?">
         <option value="single">Single-end</option>
         <option value="paired">Paired-end</option>
+        <option value="pairedCollection">Paired-end collection</option>
       </param>
       <when value="single">
         <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
@@ -62,6 +70,11 @@
         <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
         <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
       </when>
+      <when value="pairedCollection">
+          <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
+          <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
+          <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
+      </when>
     </conditional>
     
     <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" />
diff -r ddcbf8732706 -r d5464c9e1723 readme.rst
--- a/readme.rst	Mon Jan 19 12:48:51 2015 -0500
+++ b/readme.rst	Tue Mar 17 10:44:33 2015 -0400
@@ -26,6 +26,7 @@
 Version history
 ---------------
 
+- Release 4: Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
 - Release 3: Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
 - Release 2: Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.
 - Release 1: Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .