# HG changeset patch
# User jpayne
# Date 1542143897 18000
# Node ID b18e8cdfdf8183758411f5494103777b92629df5
# Parent  15572bf93a2a5dcc8fbe6ce1ae7613bd10ae2da3
planemo upload

diff -r 15572bf93a2a -r b18e8cdfdf81 seqsero2.xml
--- a/seqsero2.xml	Fri Nov 09 16:02:31 2018 -0500
+++ b/seqsero2.xml	Tue Nov 13 16:18:17 2018 -0500
@@ -11,28 +11,28 @@
       <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-      #if $reads.reads_select == 'history':
-      #set name = $reads.forward.name.split('.')[0].replace(' ','_')
-      #set forward = $reads.forward
-      #set reverse = $reads.reverse
+      #if $reads.reads_select == 'history'
+      #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
+      #set $forward = $reads.forward
+      #set $reverse = $reads.reverse
       #else
-      #set name = $reads.coll.name.replace(' ', '_')
-      #set forward = $reads.coll.forward
-      #set reverse = $reads.coll.reverse
+      #set $name = $reads.coll.name.replace(' ', '_')
+      #set $forward = $reads.coll.forward
+      #set $reverse = $reads.coll.reverse
       #end if
         echo $name ;
         echo "-=-=-=-=-" ;
-      #if forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
+      #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
         gunzip -c $forward > forward.fastq;
-      #set forward = './forward.fastq'
+      #set $forward = './forward.fastq'
       #end if
-      #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz'):
+      #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
         gunzip -c $reverse > reverse.fastq;
-      #set reverse = './reverse.fastq'
+      #set $reverse = './reverse.fastq'
       #end if
-        ln -s forward.fastq ${name}_1.fastq;
-        ln -s reverse.fastq ${name}_2.fastq;
-      mkdir ./output;
+        ln -s $forward ${name}_1.fastq;
+        ln -s $reverse ${name}_2.fastq;
+        mkdir ./output;
         python $__tool_directory__/SeqSero2/SeqSero2_package.py
         -p \${GALAXY_SLOTS:-4}
         -t 2
@@ -108,8 +108,8 @@
         <test>
          <param name="mode" value="k" />
          <param name="reads_select" value="history" />
-         <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
-         <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
+         <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
+         <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
          <output name="results" file="Seqsero_result_25k.tsv" />
        </test>
        <test>