# HG changeset patch
# User iuc
# Date 1487253011 18000
# Node ID a21dc82525395c17176c75416f93f3794a9d948c
# Parent  3c6160bd2281d24913b9ebd3f07d36da6eddab4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 379063161020578e1bd306769116c1b691216b35

diff -r 3c6160bd2281 -r a21dc8252539 hisat2.xml
--- a/hisat2.xml	Sat Jan 21 15:42:17 2017 -0500
+++ b/hisat2.xml	Thu Feb 16 08:50:11 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="2.0.3.2">
+<tool id="hisat2" name="HISAT2" version="2.0.3.3">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -7,7 +7,6 @@
     <requirements>
         <!-- Conda dependency -->
         <requirement type="package" version="2.0.3">hisat2</requirement>
-        <requirement type="package" version="2.0.3">hisat</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
     <stdio>
@@ -16,8 +15,7 @@
         <exit_code range="1:" />
     </stdio>
     <version_command>hisat2 --version</version_command>
-    <command>
-        <![CDATA[
+    <command><![CDATA[
         #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
             ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
             hisat2_extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
@@ -106,8 +104,7 @@
                 && mv '${right}' '${output_aligned_reads_r}'
             #end if
         #end if
-        ]]>
-    </command>
+    ]]></command>
     <inputs>
         <conditional name="input_format">
             <param label="Input data format" name="input_format_selector" type="select">
@@ -161,8 +158,8 @@
             <when value="advanced">
                 <param argument="-s" min="0" label="Skip the first N reads or pairs in the input" name="skip" type="integer" value="0" />
                 <param argument="-u" min="0" help="Align the first N reads or read pairs from the input (after the first N reads or pairs have been skipped), then stop." label="Stop after aligning N reads" name="stop_after" type="integer" value="0" />
-                <param argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" name="trim_five" type="integer" value="0" />
-                <param argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" name="trim_three" type="integer" value="0" />
+                <param name="trim_five" argument="-5" min="0" help="Trim N bases from 5' (left) end of each read before alignment" label="Trim 5' end" type="integer" value="0" />
+                <param name="trim_three" argument="-3" min="0" help="Trim N bases from 3' (right) end of each read before alignment" label="Trim 3' end" type="integer" value="0" />
             </when>
         </conditional>
         <conditional name="scoring_options">
diff -r 3c6160bd2281 -r a21dc8252539 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jan 21 15:42:17 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <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" />
-    </package>
-</tool_dependency>