# HG changeset patch
# User jpayne
# Date 1524686050 14400
# Node ID 62531f7399dcaa3130b7cc72a912444e78b51fb1
# Parent  11296a86e01b12c4af8768a7adc96e4489c55c62
planemo upload commit 0399c6bd696435a7a99d8d8b4c237e5a78ee5856-dirty

diff -r 11296a86e01b -r 62531f7399dc 1_map_reads.xml
--- a/1_map_reads.xml	Thu Mar 08 11:10:45 2018 -0500
+++ b/1_map_reads.xml	Wed Apr 25 15:54:10 2018 -0400
@@ -8,7 +8,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
-        env &&
         #if $reads.reads_select == 'collection'
             export files="$reads.coll.forward $reads.coll.reverse"          &&
             export params="-1 $reads.coll.forward -2 $reads.coll.reverse"   &&
@@ -81,11 +80,11 @@
                 <option value="history">Two FASTQ datasets from your history</option>
             </param>
             <when value="collection">
-                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired" />
+                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
             </when>
             <when value="history">
-                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger" />
-                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger" />
+                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
+                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
             </when>
         </conditional>
     </inputs>