# HG changeset patch
# User iuc
# Date 1464203056 14400
# Node ID 52f55ad3dee24a45a781eaf9235e375e4d065ecb
# Parent  ce5e12ebb97205aff038ad9ca62f0de7edc97d7c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8

diff -r ce5e12ebb972 -r 52f55ad3dee2 stringtie.xml
--- a/stringtie.xml	Wed Oct 21 16:06:19 2015 -0400
+++ b/stringtie.xml	Wed May 25 15:04:16 2016 -0400
@@ -4,31 +4,31 @@
         <requirement type="package" version="1.1.0">stringtie</requirement>
     </requirements>
     <command><![CDATA[
-stringtie "$input_bam"
--o "$output_gtf"
--p "\${GALAXY_SLOTS:-1}"
-#if str($guide.use_guide) == 'yes':
-    -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
-    #if str($guide.output_ballgown) == '-b':
-        $guide.output_ballgown `pwd`
-    #end if
-#end if
-#if str($option_set.options) == 'advanced':
-    -l "$option_set.name_prefix"
-    -f "$option_set.fraction"
-    -m "$option_set.min_tlen"
-    -a "$option_set.min_anchor_len"
-    -j "$option_set.min_anchor_cov"
-    -c "$option_set.min_bundle_cov"
-    -g "$option_set.bdist"
-    -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
-    #if $option_set.A:
-        -A "$gene_abundance_estimation"
-    #end if
-    #if str($option_set.x).strip() != "":
-        -x "$option_set.x"
-    #end if
-#end if
+        stringtie "$input_bam"
+            -o "$output_gtf"
+            -p "\${GALAXY_SLOTS:-1}"
+            #if str($guide.use_guide) == 'yes':
+                -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
+                #if str($guide.output_ballgown) == '-b':
+                    $guide.output_ballgown `pwd`
+                #end if
+            #end if
+            #if str($option_set.options) == 'advanced':
+                -l "$option_set.name_prefix"
+                -f "$option_set.fraction"
+                -m "$option_set.min_tlen"
+                -a "$option_set.min_anchor_len"
+                -j "$option_set.min_anchor_cov"
+                -c "$option_set.min_bundle_cov"
+                -g "$option_set.bdist"
+                -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
+                #if $option_set.A:
+                    -A "$gene_abundance_estimation"
+                #end if
+                #if str($option_set.x).strip() != "":
+                    -x "$option_set.x"
+                #end if
+            #end if
 ]]>
 </command>
     <inputs>
@@ -194,6 +194,6 @@
  ]]>
     </help>
     <citations>
-        <citation type="doi">doi:10.1038/nbt.3122</citation>
+        <citation type="doi">10.1038/nbt.3122</citation>
     </citations>
 </tool>
diff -r ce5e12ebb972 -r 52f55ad3dee2 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 21 16:06:19 2015 -0400
+++ b/tool_dependencies.xml	Wed May 25 15:04:16 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="stringtie" version="1.1.0">
-      <repository changeset_revision="5469f0f9e590" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="84784276cc2c" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>