# HG changeset patch
# User estrain
# Date 1558274825 14400
# Node ID 8bf4865cc3e3e6c6f3339f5af07e2a0ccb8e5de1
# Parent  6787d952242ee7e8bdaf23fd713098d4e11897df
Uploaded

diff -r 6787d952242e -r 8bf4865cc3e3 srst2v2.xml
--- a/srst2v2.xml	Sun May 19 07:36:55 2019 -0400
+++ b/srst2v2.xml	Sun May 19 10:07:05 2019 -0400
@@ -3,21 +3,44 @@
         <requirement type="package" version="0.2.0">srst2</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+
         #if $paired_conditional.sPaired == "paired"
-           ln -s $paired_conditional.fastq1 sample_1.fastq;
-           ln -s $paired_conditional.fastq2 sample_2.fastq;
+	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+            zcat $paired_conditional.fastq2 > sample_2.fastq;
+	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+            zcat $paired_conditional.fastq2 > sample_2.fastq;
+          #else
+            ln -s $paired_conditional.fastq1 sample_1.fastq;
+            ln -s $paired_conditional.fastq2 sample_2.fastq;
+          #end if
         #else if $paired_conditional.sPaired == "paired_coll" 
-           ln -s $paired_conditional.coll.forward sample_1.fastq;
-           ln -s $paired_conditional.coll.reverse sample_2.fastq;
+	  #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
+            zcat $paired_conditional.coll.forward > sample_1.fastq;
+            zcat $paired_conditional.coll.reverse > sample_2.fastq;
+	  #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.coll.forward > sample_1.fastq;
+            zcat $paired_conditional.coll.reverse > sample_2.fastq;
+          #else 
+            ln -s $paired_conditional.coll.forward sample_1.fastq;
+            ln -s $paired_conditional.coll.reverse sample_2.fastq;
+          #end if
+        #else if $paired_conditional.sPaired == "single"
+	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
+            zcat $paired_conditional.fastq1 > sample_1.fastq;
+          #else
+            ln -s $paired_conditional.fastq1 sample_1.fastq;
+          #end if
         #end if
 
         srst2
 
         #if $paired_conditional.sPaired == "single"
-            --input_se $paired_conditional.fastq1
-        #else if $paired_conditional.sPaired == "paired"
-            --input_pe sample_1.fastq sample_2.fastq
-        #else if $paired_conditional.sPaired == "paired_coll"
+            --input_se sample_1.fastq1
+        #else
             --input_pe sample_1.fastq sample_2.fastq
         #end if