# HG changeset patch
# User devteam
# Date 1444754005 14400
# Node ID af089ca8b4ee3f06cfdf02363f061b747d245cf2
# Parent 51c6602b46b9bed92f92fe16118ebe2a007de927
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
diff -r 51c6602b46b9 -r af089ca8b4ee tool_dependencies.xml
--- a/tool_dependencies.xml Thu Jan 23 12:30:49 2014 -0500
+++ b/tool_dependencies.xml Tue Oct 13 12:33:25 2015 -0400
@@ -1,12 +1,12 @@
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diff -r 51c6602b46b9 -r af089ca8b4ee tophat_wrapper.xml
--- a/tophat_wrapper.xml Thu Jan 23 12:30:49 2014 -0500
+++ b/tophat_wrapper.xml Tue Oct 13 12:33:25 2015 -0400
@@ -1,5 +1,5 @@
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Find splice junctions using RNA-seq data
tophat --version
@@ -43,7 +43,7 @@
--seg-mismatches=$singlePaired.sParams.seg_mismatches
--seg-length=$singlePaired.sParams.seg_length
--library-type=$singlePaired.sParams.library_type
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## Indel search.
#if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
## --allow-indels
@@ -104,7 +104,7 @@
--seg-mismatches=$singlePaired.pParams.seg_mismatches
--seg-length=$singlePaired.pParams.seg_length
--library-type=$singlePaired.pParams.library_type
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## Indel search.
#if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
## --allow-indels
@@ -181,25 +181,14 @@
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-alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
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@@ -234,7 +223,7 @@
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@@ -402,7 +391,7 @@
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