# HG changeset patch
# User iuc
# Date 1424277430 18000
# Node ID ab4798cf6458262831c71ccbcbb7b2880eb2e886
# Parent  f5c030adcdedf03457b17ac11f20b8a10ff28174
Uploaded

diff -r f5c030adcded -r ab4798cf6458 stringtie.xml
--- a/stringtie.xml	Tue Jul 01 19:08:39 2014 -0400
+++ b/stringtie.xml	Wed Feb 18 11:37:10 2015 -0500
@@ -47,7 +47,6 @@
             <when value="advanced">
                 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />
                 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />
-                <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" />
                 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
                 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />
                 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />
@@ -103,15 +102,13 @@
    -s  coverage saturation threshold; further read alignments will be
        ignored in a region where a local coverage depth of <maxcov>
        is reached (default: 1,000,000);
-   -v  verbose (log bundle processing details)
    -e  abundance estimation only of input transcripts (for -G option)
    -g  gap between read mappings triggering a new bundle (default: 50)
    -S  more sensitive run (default: no)
    -C  output file with all transcripts in reference that are fully
        covered by reads
    -M  fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
-   -p  number of threads (CPUs) to use (default: 1)
 
 ]]>
 </help>
-</tool>
\ No newline at end of file
+</tool>
diff -r f5c030adcded -r ab4798cf6458 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 01 19:08:39 2014 -0400
+++ b/tool_dependencies.xml	Wed Feb 18 11:37:10 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="stringtie" version="0.97">
-      <repository changeset_revision="09b1ece7f3e9" name="package_stringtie_0_97" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="0627e8e30873" name="package_stringtie_0_97" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>