# HG changeset patch
# User sanbi-uwc
# Date 1498556446 14400
# Node ID 77814664cb3f7c04e77046052d862c0732c3b178
# Parent  94ae1dd64bca46ec7eee4c01cb7ac4a65bfb3949
planemo upload for repository https://github.com/zipho/novo_align commit 5bc8cfdb572731dea908d62f22b080b1534ddedb

diff -r 94ae1dd64bca -r 77814664cb3f novo_align.xml
--- a/novo_align.xml	Fri Jan 20 08:45:45 2017 -0500
+++ b/novo_align.xml	Tue Jun 27 05:40:46 2017 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8" ?>
-<tool id="novo_align" name="NOVO ALIGN" version="0.0.8">
+<tool id="novo_align" name="NOVO ALIGN" version="0.0.9">
     <description>Tool to run the Novo Align mapping tool</description>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>
@@ -46,7 +46,7 @@
             '${out_file}'
             --index
             #if str($index.source) == 'builtin':
-              '${index.index1}'
+              '${index.index1.fields.path}'
             #else
               reference.nix
             #end if
@@ -77,7 +77,7 @@
     <conditional name="paired_end">
     <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="yes" />
     <when value="no">
-      <param name="fastq_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file" />
+      <param name="fastq_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file" />
     </when>
     <when value="yes">
       <conditional name="paired_input_type_conditional">
@@ -86,11 +86,11 @@
           <option value="collection">Dataset collection pair</option>
         </param>
         <when value="pair_of_files">
-      <param name="fastq_r1_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file (R1/first of pair)" />
-      <param name="fastq_r2_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file (R2/second of pair)" />
+      <param name="fastq_r1_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file (R1/first of pair)" />
+      <param name="fastq_r2_in" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ file (R2/second of pair)" />
     </when>
         <when value="collection">
-          <param name="fastq_pair" format="fastqsanger|fastqsanger.gz" type="data_collection"
+          <param name="fastq_pair" format="fastqsanger,fastqsanger.gz" type="data_collection"
          collection_type="paired"
          label="Select FASTQ dataset collection with R1/R2 pair" />
         </when>