Mercurial > repos > lparsons > htseq_count

changeset 17:d5edaf8dc974 draft

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Fixed test output, added missing pysam dependency
author lparsons
date Fri, 11 Apr 2014 16:01:54 -0400
parents 227f9d3f0e32
children 087e32034c95
files htseq-count.xml test-data/htseq-test-paired_othercounts.tsv test-data/htseq-test_othercounts.tsv tool_dependencies.xml
diffstat 4 files changed, 16 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/htseq-count.xml	Fri Apr 11 15:05:28 2014 -0400
+++ b/htseq-count.xml	Fri Apr 11 16:01:54 2014 -0400
@@ -1,10 +1,11 @@
-<tool id="htseq_count" name="htseq-count" version="0.4">
+<tool id="htseq_count" name="htseq-count" version="0.4.1">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
         <requirement type="package" version="1.7.1">numpy</requirement>
         <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
     </requirements>
     <command>
     ##set up input files
--- a/test-data/htseq-test-paired_othercounts.tsv	Fri Apr 11 15:05:28 2014 -0400
+++ b/test-data/htseq-test-paired_othercounts.tsv	Fri Apr 11 16:01:54 2014 -0400
@@ -1,5 +1,5 @@
-no_feature	533
-ambiguous	1
-too_low_aQual	0
-not_aligned	0
-alignment_not_unique	0
+_feature	755
+__ambiguous	0
+__too_low_aQual	96
+__not_aligned	0
+__alignment_not_unique	0
--- a/test-data/htseq-test_othercounts.tsv	Fri Apr 11 15:05:28 2014 -0400
+++ b/test-data/htseq-test_othercounts.tsv	Fri Apr 11 16:01:54 2014 -0400
@@ -1,5 +1,5 @@
-no_feature	19
-ambiguous	0
-too_low_aQual	0
-not_aligned	1336
-alignment_not_unique	0
+__no_feature	19
+__ambiguous	0
+__too_low_aQual	0
+__not_aligned	1336
+__alignment_not_unique	0
--- a/tool_dependencies.xml	Fri Apr 11 15:05:28 2014 -0400
+++ b/tool_dependencies.xml	Fri Apr 11 16:01:54 2014 -0400
@@ -9,6 +9,10 @@
         <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+
     <package name="htseq" version="0.6.1">
         <install version="1.0">
             <actions>