Changeset 988:43e5a0b863d3

Timestamp:

02/22/08 15:09:25 (11 months ago)

Author:

Greg Von Kuster <greg@bx.psu.edu>

branch:

default

convert_revision:

svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2345

Message:

Added tool version directories to regVariation tools directory.

Files:

• tool_conf.xml.main (modified) (1 diff)
• tool_conf.xml.sample (modified) (1 diff)
• tools/regVariation/coverage.py (deleted)
• tools/regVariation/cpgFilter/1.0.0/maf_cpg_filter.py (moved) (moved from tools/regVariation/maf_cpg_filter.py)
• tools/regVariation/cpgFilter/1.0.0/maf_cpg_filter.xml (moved) (moved from tools/regVariation/maf_cpg_filter.xml)
• tools/regVariation/featureCounter_LIST.py (deleted)
• tools/regVariation/featureCounter_OLD.py (deleted)
• tools/regVariation/featureCounter_OLD2.py (deleted)
• tools/regVariation/featureCounter_code.py (deleted)
• tools/regVariation/featureCoverage1/1.0.0/featureCounter.py (moved) (moved from tools/regVariation/featureCounter.py) (1 diff)
• tools/regVariation/featureCoverage1/1.0.0/featureCounter.xml (moved) (moved from tools/regVariation/featureCounter.xml)
• tools/regVariation/galaxyops/__init__.py (deleted)
• tools/regVariation/getIndels_2way/1.0.0/getIndels.py (moved) (moved from tools/regVariation/getIndels.py)
• tools/regVariation/getIndels_2way/1.0.0/getIndels_2way.xml (moved) (moved from tools/regVariation/getIndels_2way.xml)
• tools/regVariation/getIndels_3way/1.0.0/getIndels_3way.xml (moved) (moved from tools/regVariation/getIndels_3way.xml)
• tools/regVariation/getIndels_3way/1.0.0/parseMAF_smallIndels.pl (moved) (moved from tools/regVariation/parseMAF_smallIndels.pl)
• tools/regVariation/getIndels_good_11_19.py (deleted)
• tools/regVariation/getIndels_old.py (deleted)
• tools/regVariation/maf_index_entry.py (deleted)
• tools/regVariation/qa_scores_by_chr.py (deleted)
• tools/regVariation/qualityFilter/1.0.0/quality_filter.py (moved) (moved from tools/regVariation/quality_filter.py)
• tools/regVariation/qualityFilter/1.0.0/quality_filter.xml (moved) (moved from tools/regVariation/quality_filter.xml)
• tools/regVariation/qv2bqv/1.0.0/qv_to_bqv.py (moved) (moved from tools/regVariation/qv_to_bqv.py)
• tools/regVariation/qv2bqv/1.0.0/qv_to_bqv.xml (moved) (moved from tools/regVariation/qv_to_bqv.xml)
• tools/regVariation/winSplitter/1.0.0/windowSplitter.py (moved) (moved from tools/regVariation/windowSplitter.py) (1 diff)
• tools/regVariation/winSplitter/1.0.0/windowSplitter.xml (moved) (moved from tools/regVariation/windowSplitter.xml)

tool_conf.xml.main

@@ -118 +118 @@
-  </section>
-  <section name="Regional Variation" id="regVar">
-
-
-
-
+Splitter/1.0.0/win
+verage1/1.0.0/featureCo
+Filter/1.0.0/quality
+cpgFilter/1.0.0/
-        <!--
-
-
+/1.0.0/getIndels_2way
+/1.0.0/getIndels_3way
-        -->
-  </section>

tool_conf.xml.sample

@@ -123 +123 @@
-  </section>
-  <section name="Regional Variation" id="regVar">
-
-
-
-
-
-
+Splitter/1.0.0/win
+verage1/1.0.0/featureCo
+Filter/1.0.0/quality
+cpgFilter/1.0.0/
+/1.0.0/getIndels_2way
+/1.0.0/getIndels_3way
-  </section>
- <section name="Evolution: HyPhy" id="hyphy">

tools/regVariation/featureCoverage1/1.0.0/featureCounter.py

@@ -23 +23 @@
-from bx.cookbook import doc_optparse
-
-
+.tools.util.galaxy
-
-def stop_err(msg):

tools/regVariation/winSplitter/1.0.0/windowSplitter.py

@@ -12 +12 @@
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
-
+.tools.util.galaxy
-
-def main():