# HG changeset patch
# User iuc
# Date 1460579896 14400
# Node ID 67e9ee942e54a103bd48f38e9a621c8bb303c012
# Parent  fd42a1fdc101260738635b5ae6231c2b87a2c02c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 64b86fe2d6708fadebe6b05fc5ae520046f870f4

diff -r fd42a1fdc101 -r 67e9ee942e54 hisat2.xml
--- a/hisat2.xml	Tue Mar 15 13:02:47 2016 -0400
+++ b/hisat2.xml	Wed Apr 13 16:38:16 2016 -0400
@@ -1,13 +1,12 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="1.0.1">
+<tool id="hisat2" name="HISAT" version="2.0.3">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="2.0">hisat</requirement>
         <!-- Conda dependency -->
-        <requirement type="package" version="2.0.0beta">hisat2</requirement>
+        <requirement type="package" version="2.0.3">hisat2</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <stdio>
@@ -252,7 +251,7 @@
             <param ftype="fasta" name="history_item" value="phiX.fa" />
             <param ftype="fastqsanger" name="reads_f" value="hisat_input_1_forward.fastq" />
             <param ftype="fastqsanger" name="reads_r" value="hisat_input_1_reverse.fastq" />
-            <output file="hisat_output_1.bam" ftype="bam" name="output_alignments" />
+            <output file="hisat_output_1.bam" ftype="bam" name="output_alignments" lines_diff="2" />
         </test>
         <test>
             <param name="input_format_selector" value="fastq" />
@@ -264,7 +263,7 @@
             <param name="trim_five" value="15" />
             <param ftype="fastqsanger" name="reads_f" value="hisat_input_2_forward.fastq" />
             <param ftype="fastqsanger" name="reads_r" value="hisat_input_2_reverse.fastq" />
-            <output file="hisat_output_2.bam" ftype="bam" name="output_alignments" />
+            <output file="hisat_output_2.bam" ftype="bam" name="output_alignments" lines_diff="2" />
         </test>
         <test>
             <param name="input_format_selector" value="fastq" />
@@ -279,7 +278,7 @@
             <param name="paired_end_options_selector" value="advanced" />
             <param name="no_mixed" value="True" />
             <param name="no_discordant" value="True" />
-            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" />
+            <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" />
         </test>
     </tests>
     <help>
diff -r fd42a1fdc101 -r 67e9ee942e54 test-data/hisat_output_1.bam
Binary file test-data/hisat_output_1.bam has changed
diff -r fd42a1fdc101 -r 67e9ee942e54 test-data/hisat_output_2.bam
Binary file test-data/hisat_output_2.bam has changed
diff -r fd42a1fdc101 -r 67e9ee942e54 test-data/hisat_output_3.bam
Binary file test-data/hisat_output_3.bam has changed
diff -r fd42a1fdc101 -r 67e9ee942e54 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Mar 15 13:02:47 2016 -0400
+++ b/tool_dependencies.xml	Wed Apr 13 16:38:16 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="hisat" version="2.0">
-        <repository changeset_revision="0f7f6f91aaee" name="package_hisat_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="hisat" version="2.0.3">
+        <repository changeset_revision="92cab2ab7948" name="package_hisat_2_0_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="1.2">
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />