# HG changeset patch
# User iuc
# Date 1439377660 14400
# Node ID df42808cc33abc8fbfee413e3aabcc162cb3e948
# Parent  48b891c1c2aa55f2f4490910afc9424918cd8f7c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf

diff -r 48b891c1c2aa -r df42808cc33a stringtie.xml
--- a/stringtie.xml	Thu May 14 12:36:35 2015 -0400
+++ b/stringtie.xml	Wed Aug 12 07:07:40 2015 -0400
@@ -1,7 +1,7 @@
-<tool id="stringtie" name="StringTie" version="1.0.3">
+<tool id="stringtie" name="StringTie" version="1.0.4">
     <description>transcript assembly and quantification</description>
     <requirements>
-        <requirement type="package" version="1.0.3">stringtie</requirement>
+        <requirement type="package" version="1.0.4">stringtie</requirement>
     </requirements>
     <command><![CDATA[
 stringtie "$input_bam"
@@ -21,7 +21,7 @@
     -j "$option_set.min_anchor_cov"
     -c "$option_set.min_bundle_cov"
     -s "$option_set.maxcov"
-    -g "$option_set.bdist"    
+    -g "$option_set.bdist"
     -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
 #end if
 ]]>
@@ -87,21 +87,21 @@
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="default" />
-            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
-            <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="yes" />
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="default" />
-            <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
@@ -109,7 +109,7 @@
             <param name="guide_gff" value="stringtie_in.gtf" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
-            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
         </test>
         <test>
             <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
@@ -122,7 +122,7 @@
             <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
             <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
             <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
-            <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
             <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
         </test>
     </tests>
diff -r 48b891c1c2aa -r df42808cc33a test-data/ballgown/e_data.ctab
--- a/test-data/ballgown/e_data.ctab	Thu May 14 12:36:35 2015 -0400
+++ b/test-data/ballgown/e_data.ctab	Wed Aug 12 07:07:40 2015 -0400
@@ -1,4 +1,4 @@
 e_id	chr	strand	start	end	rcount	ucount	mrcount	cov	cov_sd	mcov	mcov_sd
-1	test_chromosome	+	53	250	154	154	154.00	49.7778	22.0747	49.7778	22.0747
+1	test_chromosome	+	53	250	158	158	158.00	49.7778	22.0747	49.7778	22.0747
 2	test_chromosome	+	351	400	73	73	73.00	54.1600	6.1753	54.1600	6.1753
 3	test_chromosome	+	501	550	38	38	38.00	21.6400	12.4350	21.6400	12.4350
diff -r 48b891c1c2aa -r df42808cc33a tool_dependencies.xml
--- a/tool_dependencies.xml	Thu May 14 12:36:35 2015 -0400
+++ b/tool_dependencies.xml	Wed Aug 12 07:07:40 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="stringtie" version="1.0.3">
-      <repository changeset_revision="76595a6609c0" name="package_stringtie_1_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="stringtie" version="1.0.4">
+      <repository changeset_revision="f3818f4bc127" name="package_stringtie_1_0_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>