# HG changeset patch
# User gbcs-embl-heidelberg
# Date 1505477868 14400
# Node ID dacd089d81ae50f2343b09bba6a23599792f13fa
# Parent  222819c87d905cf0336d0ed73acc3e412c60772c
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0

diff -r 222819c87d90 -r dacd089d81ae macros.xml
--- a/macros.xml	Wed Aug 02 10:59:28 2017 -0400
+++ b/macros.xml	Fri Sep 15 08:17:48 2017 -0400
@@ -27,8 +27,8 @@
 
     <xml name="paired_options">
         <when value="paired">
-            <param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/>
-            <param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/>
+            <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #1"/>
+            <param name="input_2" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #2"/>
             <yield />
             <param name="SAME_HEADERS" type="boolean"
                 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
@@ -37,7 +37,7 @@
                 falsevalue="false" checked="false"/>
         </when>
         <when value="paired_collection">
-            <param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired"
+            <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
                 label="FASTQ Paired Dataset"/>
             <yield />
             <param name="SAME_HEADERS" type="boolean"
@@ -70,18 +70,18 @@
               <option value="paired_collection">Paired-end Dataset Collection</option>
             </param>
             <when value="single">
-                <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
-                <param name="I1" type="data" format="fastq,gz" label="First Index File"/>
+                <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
+                <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
             </when>
             <expand macro="paired_options">
-                <param name="I1" type="data" format="fastq,gz" label="First Index File"/>
+                <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/>
                 <conditional name="I2_CONDITIONAL">
                     <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
                         <option value="true">Yes</option>
                         <option value="false" selected="true">No</option>
                     </param>
                     <when value="true">
-                        <param name="I2" type="data" format="fastq,gz" label="Second Index File"/>
+                        <param name="I2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Second Index File"/>
                         <expand macro="bred_conditional"/>
                     </when>
                     <when value="false"/>
@@ -98,7 +98,7 @@
               <option value="paired_collection">Paired-end Dataset Collection</option>
             </param>
             <when value="single">
-                <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/>
+                <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/>
             </when>
             <expand macro="paired_options">
                 <yield />
diff -r 222819c87d90 -r dacd089d81ae test-data/illu_summary_PE.txt
--- a/test-data/illu_summary_PE.txt	Wed Aug 02 10:59:28 2017 -0400
+++ b/test-data/illu_summary_PE.txt	Fri Sep 15 08:17:48 2017 -0400
@@ -4,8 +4,8 @@
 Assigned Reads (pairs)	10
 Unassigned Reads (pairs)	15
 # Individual sample read (pair) counts :
-emb681m1	2
 emb681m4	2
 emb681m5	2
+emb681m1	2
+emb6801m1	2
 emb6801m2	2
-emb6801m1	2