1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/199767a1714b/ changeset: 199767a1714b user: jgoecks date: 2012-09-26 16:30:59 summary: Bump version support for Cuffcompare, Cuffmerge to v2.0 and increase lines_diff to prevent Cuffmerge test from failing due to non-deterministic output. affected #: 4 files

diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py +++ b/tools/ngs_rna/cuffcompare_wrapper.py @@ -1,5 +1,7 @@ #!/usr/bin/env python

+# Supports Cuffcompare versions v1.3.0 and newer. + import optparse, os, shutil, subprocess, sys, tempfile

def stop_err( msg ):

diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffcompare" name="Cuffcompare" version="0.0.5"> - <!-- Wrapper supports Cuffcompare versions v1.0.0-v1.3.0 --> + <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer --><description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description><requirements><requirement type="package">cufflinks</requirement>

diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -1,5 +1,7 @@ #!/usr/bin/env python

+# Supports Cuffmerge versions 1.3 and newer. + import optparse, os, shutil, subprocess, sys, tempfile

def stop_err( msg ):

diff -r cfd6428269c88c4690d644929969e852af672f45 -r 199767a1714b27a9a5c3f2376ad0133a70cd7c51 tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -1,5 +1,5 @@ <tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> - <!-- Wrapper supports Cuffmerge version v1.0.0 --> + <!-- Wrapper supports Cuffmerge versions 1.3 and newer --><description>merge together several Cufflinks assemblies</description><requirements><requirement type="package">cufflinks</requirement> @@ -88,7 +88,7 @@ <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="use_seq_data" value="No"/><!-- oId assignment differ/are non-deterministic --> - <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="8"/> + <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/></test></tests>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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