# HG changeset patch
# User devteam
# Date 1437507192 14400
# Node ID 8bb3efa0dae8bd9e221eaaf0b4499a9485e94797
# Parent  e3fe061597acc50993ad4322acc7640a07934c99
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 8000b1dd0d6b336707cf84867d11f690f6a26f5c

diff -r e3fe061597ac -r 8bb3efa0dae8 hisat.xml
--- a/hisat.xml	Thu Jun 11 16:35:16 2015 -0400
+++ b/hisat.xml	Tue Jul 21 15:33:12 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="hisat" name="HISAT" version="1.0.1">
+<tool id="hisat" name="HISAT" version="1.0.2">
     <description>spliced aligner</description>
     <macros>
         <import>hisat_macros.xml</import>
@@ -12,9 +12,9 @@
     </stdio>
     <version_command>hisat --version</version_command>
     <command><![CDATA[
-        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gff) != 'None':
-            ln -s "${spliced_options.known_splice_gff}" splice_sites.gff &&
-            extract_splice_sites.py splice_sites.gff > splice_sites.txt &&
+        #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != 'None':
+            ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&
+            extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&
         #end if
         #if $reference_genome.reference_genome_source == "history":
             ln -s "$reference_genome.history_item" genome.fa &&
@@ -58,7 +58,7 @@
         #if str($spliced_options.spliced_options_selector) == "advanced":
             --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
             --pen-intronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient_term}
-            #if str($spliced_options.known_splice_gff) != 'None':
+            #if str($spliced_options.known_splice_gtf) != 'None':
                 --known-splicesite-infile splice_sites.txt
             #end if
         #end if
@@ -183,7 +183,7 @@
                 </expand>
                 <param name="min_intron" label="Minimum intron length" type="integer" value="20" />
                 <param name="max_intron" label="Maximum intron length" type="integer" value="500000" />
-                <param name="known_splice_gff" label="GTF/GFF file with known splice sites" type="data" format="gff" optional="True" />
+                <param name="known_splice_gtf" label="GTF file with known splice sites" type="data" format="gtf" optional="True" />
             </when>
         </conditional>
     </inputs>
diff -r e3fe061597ac -r 8bb3efa0dae8 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jun 11 16:35:16 2015 -0400
+++ b/tool_dependencies.xml	Tue Jul 21 15:33:12 2015 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="e1f428b67305" name="package_hisat_0_1_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="1.2">
-        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>