From 99bc8db3fda6125cef463ac566d7690243c1e06d Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Fri, 22 Feb 2008 19:23:18 +0000
Subject: [PATCH] Added tool version directories to new_operations tools
 directory.

---
 .../galaxy/tools/util}/galaxyops/__init__.py  |  0
 tool_conf.xml.main                            | 22 +++++++++----------
 tool_conf.xml.sample                          | 22 +++++++++----------
 .../{ => get_flanks1/1.0.0}/get_flanks.py     |  2 +-
 .../{ => get_flanks1/1.0.0}/get_flanks.xml    |  0
 .../1.0.0}/basecoverage.xml                   |  2 +-
 .../1.0.0}/gops_basecoverage.py               |  2 +-
 .../{ => gops_cluster_1/1.0.0}/cluster.xml    |  2 +-
 .../1.0.0}/gops_cluster.py                    |  2 +-
 .../1.0.0}/complement.xml                     |  2 +-
 .../1.0.0}/gops_complement.py                 |  2 +-
 .../{ => gops_concat_1/1.0.0}/concat.xml      |  2 +-
 .../{ => gops_concat_1/1.0.0}/gops_concat.py  |  2 +-
 .../{ => gops_coverage_1/1.0.0}/coverage.xml  |  2 +-
 .../1.0.0}/gops_coverage.py                   |  2 +-
 .../1.0.0}/gops_intersect.py                  |  2 +-
 .../1.0.0}/intersect.xml                      |  2 +-
 .../{ => gops_join_1/1.0.0}/gops_join.py      |  2 +-
 .../{ => gops_join_1/1.0.0}/join.xml          |  2 +-
 .../{ => gops_merge_1/1.0.0}/gops_merge.py    |  2 +-
 .../{ => gops_merge_1/1.0.0}/merge.xml        |  2 +-
 .../1.0.0}/gops_subtract.py                   |  2 +-
 .../{ => gops_subtract_1/1.0.0}/subtract.xml  |  2 +-
 .../1.0.0}/subtract_query.py                  |  0
 .../1.0.0}/subtract_query.xml                 |  0
 25 files changed, 41 insertions(+), 41 deletions(-)
 rename {tools/new_operations => lib/galaxy/tools/util}/galaxyops/__init__.py (100%)
 rename tools/new_operations/{ => get_flanks1/1.0.0}/get_flanks.py (99%)
 rename tools/new_operations/{ => get_flanks1/1.0.0}/get_flanks.xml (100%)
 rename tools/new_operations/{ => gops_basecoverage_1/1.0.0}/basecoverage.xml (96%)
 rename tools/new_operations/{ => gops_basecoverage_1/1.0.0}/gops_basecoverage.py (97%)
 rename tools/new_operations/{ => gops_cluster_1/1.0.0}/cluster.xml (98%)
 rename tools/new_operations/{ => gops_cluster_1/1.0.0}/gops_cluster.py (99%)
 rename tools/new_operations/{ => gops_complement_1/1.0.0}/complement.xml (97%)
 rename tools/new_operations/{ => gops_complement_1/1.0.0}/gops_complement.py (98%)
 rename tools/new_operations/{ => gops_concat_1/1.0.0}/concat.xml (97%)
 rename tools/new_operations/{ => gops_concat_1/1.0.0}/gops_concat.py (98%)
 rename tools/new_operations/{ => gops_coverage_1/1.0.0}/coverage.xml (98%)
 rename tools/new_operations/{ => gops_coverage_1/1.0.0}/gops_coverage.py (98%)
 rename tools/new_operations/{ => gops_intersect_1/1.0.0}/gops_intersect.py (98%)
 rename tools/new_operations/{ => gops_intersect_1/1.0.0}/intersect.xml (96%)
 rename tools/new_operations/{ => gops_join_1/1.0.0}/gops_join.py (98%)
 rename tools/new_operations/{ => gops_join_1/1.0.0}/join.xml (99%)
 rename tools/new_operations/{ => gops_merge_1/1.0.0}/gops_merge.py (98%)
 rename tools/new_operations/{ => gops_merge_1/1.0.0}/merge.xml (97%)
 rename tools/new_operations/{ => gops_subtract_1/1.0.0}/gops_subtract.py (98%)
 rename tools/new_operations/{ => gops_subtract_1/1.0.0}/subtract.xml (98%)
 rename tools/new_operations/{ => subtract_query1/1.0.0}/subtract_query.py (100%)
 rename tools/new_operations/{ => subtract_query1/1.0.0}/subtract_query.xml (100%)

diff --git a/tools/new_operations/galaxyops/__init__.py b/lib/galaxy/tools/util/galaxyops/__init__.py
similarity index 100%
rename from tools/new_operations/galaxyops/__init__.py
rename to lib/galaxy/tools/util/galaxyops/__init__.py
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 9e5f5e62ebb..3b18735b5d7 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -44,7 +44,7 @@
   <section name="Join, Subtract and Group" id="group">
     <tool file="filters/join1/2.0.0/joiner.xml" />
     <tool file="filters/comp1/1.0.0/compare.xml"/>
-    <tool file="new_operations/subtract_query.xml"/>
+    <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
     <tool file="stats/grouping.xml" />   
   </section>
   <section name="Convert Formats" id="convert">
@@ -93,16 +93,16 @@
     <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
-  	<tool file="new_operations/intersect.xml" id="intersect" />  
-    <tool file="new_operations/subtract.xml" id="subtract" />
-    <tool file="new_operations/merge.xml" id="merge" />
-    <tool file="new_operations/concat.xml" id="concat" />
-    <tool file="new_operations/basecoverage.xml" id="basecoverage" />
-    <tool file="new_operations/coverage.xml" id="coverage" />
-    <tool file="new_operations/complement.xml" id="complement" />
-    <tool file="new_operations/cluster.xml" id="cluster" />
-    <tool file="new_operations/join.xml" id="join" />
-    <tool file="new_operations/get_flanks.xml" />
+  	<tool file="new_operations/gops_intersect_1/1.0.0/intersect.xml" />  
+    <tool file="new_operations/gops_subtract_1/1.0.0/subtract.xml" id="subtract" />
+    <tool file="new_operations/gops_merge_1/1.0.0/merge.xml" id="merge" />
+    <tool file="new_operations/gops_concat_1/1.0.0/concat.xml" id="concat" />
+    <tool file="new_operations/gops_basecoverage_1/1.0.0/basecoverage.xml" />
+    <tool file="new_operations/gops_coverage_1/1.0.0/coverage.xml" id="coverage" />
+    <tool file="new_operations/gops_complement_1/1.0.0/complement.xml" id="complement" />
+    <tool file="new_operations/gops_cluster_1/1.0.0/cluster.xml" id="cluster" />
+    <tool file="new_operations/gops_join_1/1.0.0/join.xml" id="join" />
+    <tool file="new_operations/get_flanks1/1.0.0/get_flanks.xml" />
   </section>
   <section name="Statistics" id="stats">
     <tool file="stats/gsummary.xml" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index 6006e6f0b42..63bcdd43143 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -48,7 +48,7 @@
   <section name="Join, Subtract and Group" id="group">
     <tool file="filters/join1/2.0.0/joiner.xml" />
     <tool file="filters/comp1/1.0.0/compare.xml"/>
-    <tool file="new_operations/subtract_query.xml"/>
+    <tool file="new_operations/subtract_query1/1.0.0/subtract_query.xml"/>
     <tool file="stats/grouping.xml" />   
   </section>
   <section name="Convert Formats" id="convert">
@@ -97,16 +97,16 @@
     <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
-  	<tool file="new_operations/intersect.xml" id="intersect" />  
-    <tool file="new_operations/subtract.xml" id="subtract" />
-    <tool file="new_operations/merge.xml" id="merge" />
-    <tool file="new_operations/concat.xml" id="concat" />
-    <tool file="new_operations/basecoverage.xml" id="basecoverage" />
-    <tool file="new_operations/coverage.xml" id="coverage" />
-    <tool file="new_operations/complement.xml" id="complement" />
-    <tool file="new_operations/cluster.xml" id="cluster" />
-    <tool file="new_operations/join.xml" id="join" />
-    <tool file="new_operations/get_flanks.xml" />
+  	<tool file="new_operations/gops_intersect_1/1.0.0/intersect.xml" />  
+    <tool file="new_operations/gops_subtract_1/1.0.0/subtract.xml" id="subtract" />
+    <tool file="new_operations/gops_merge_1/1.0.0/merge.xml" id="merge" />
+    <tool file="new_operations/gops_concat_1/1.0.0/concat.xml" id="concat" />
+    <tool file="new_operations/gops_basecoverage_1/1.0.0/basecoverage.xml" />
+    <tool file="new_operations/gops_coverage_1/1.0.0/coverage.xml" id="coverage" />
+    <tool file="new_operations/gops_complement_1/1.0.0/complement.xml" id="complement" />
+    <tool file="new_operations/gops_cluster_1/1.0.0/cluster.xml" id="cluster" />
+    <tool file="new_operations/gops_join_1/1.0.0/join.xml" id="join" />
+    <tool file="new_operations/get_flanks1/1.0.0/get_flanks.xml" />
   </section>
   <section name="Statistics" id="stats">
     <tool file="stats/gsummary.xml" />
diff --git a/tools/new_operations/get_flanks.py b/tools/new_operations/get_flanks1/1.0.0/get_flanks.py
similarity index 99%
rename from tools/new_operations/get_flanks.py
rename to tools/new_operations/get_flanks1/1.0.0/get_flanks.py
index fbd2696058b..807b6c21c7f 100644
--- a/tools/new_operations/get_flanks.py
+++ b/tools/new_operations/get_flanks1/1.0.0/get_flanks.py
@@ -12,7 +12,7 @@ usage: %prog input out_file size direction region
 import sys, sets, re, os
 import pkg_resources; pkg_resources.require( "bx-python" )
 from bx.cookbook import doc_optparse
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def stop_err( msg ):
     sys.stderr.write( msg )
diff --git a/tools/new_operations/get_flanks.xml b/tools/new_operations/get_flanks1/1.0.0/get_flanks.xml
similarity index 100%
rename from tools/new_operations/get_flanks.xml
rename to tools/new_operations/get_flanks1/1.0.0/get_flanks.xml
diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/gops_basecoverage_1/1.0.0/basecoverage.xml
similarity index 96%
rename from tools/new_operations/basecoverage.xml
rename to tools/new_operations/gops_basecoverage_1/1.0.0/basecoverage.xml
index 3cff9258a7b..0e3b81ece20 100644
--- a/tools/new_operations/basecoverage.xml
+++ b/tools/new_operations/gops_basecoverage_1/1.0.0/basecoverage.xml
@@ -9,7 +9,7 @@
   <outputs>
     <data format="txt" name="output" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_basecoverage.py b/tools/new_operations/gops_basecoverage_1/1.0.0/gops_basecoverage.py
similarity index 97%
rename from tools/new_operations/gops_basecoverage.py
rename to tools/new_operations/gops_basecoverage_1/1.0.0/gops_basecoverage.py
index 28bac9bf45a..a706f1d6eeb 100644
--- a/tools/new_operations/gops_basecoverage.py
+++ b/tools/new_operations/gops_basecoverage_1/1.0.0/gops_basecoverage.py
@@ -20,7 +20,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.base_coverage import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/gops_cluster_1/1.0.0/cluster.xml
similarity index 98%
rename from tools/new_operations/cluster.xml
rename to tools/new_operations/gops_cluster_1/1.0.0/cluster.xml
index 03020674f05..b985dc19450 100644
--- a/tools/new_operations/cluster.xml
+++ b/tools/new_operations/gops_cluster_1/1.0.0/cluster.xml
@@ -22,7 +22,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py">
+  <code file="../../operation_filter.py">
     <hook exec_after_process="exec_after_cluster" />
   </code>
   <tests>
diff --git a/tools/new_operations/gops_cluster.py b/tools/new_operations/gops_cluster_1/1.0.0/gops_cluster.py
similarity index 99%
rename from tools/new_operations/gops_cluster.py
rename to tools/new_operations/gops_cluster_1/1.0.0/gops_cluster.py
index 0b695781fdb..6a8f8d0724c 100644
--- a/tools/new_operations/gops_cluster.py
+++ b/tools/new_operations/gops_cluster_1/1.0.0/gops_cluster.py
@@ -24,7 +24,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.find_clusters import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
     distance = 0
diff --git a/tools/new_operations/complement.xml b/tools/new_operations/gops_complement_1/1.0.0/complement.xml
similarity index 97%
rename from tools/new_operations/complement.xml
rename to tools/new_operations/gops_complement_1/1.0.0/complement.xml
index cd5350a0d04..c3ea07e769c 100644
--- a/tools/new_operations/complement.xml
+++ b/tools/new_operations/gops_complement_1/1.0.0/complement.xml
@@ -11,7 +11,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_complement.py b/tools/new_operations/gops_complement_1/1.0.0/gops_complement.py
similarity index 98%
rename from tools/new_operations/gops_complement.py
rename to tools/new_operations/gops_complement_1/1.0.0/gops_complement.py
index 802a5b06913..8c67b66b9c0 100644
--- a/tools/new_operations/gops_complement.py
+++ b/tools/new_operations/gops_complement_1/1.0.0/gops_complement.py
@@ -23,7 +23,7 @@ from bx.intervals.operations.complement import complement
 from bx.intervals.operations.subtract import subtract
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
     allchroms = False
diff --git a/tools/new_operations/concat.xml b/tools/new_operations/gops_concat_1/1.0.0/concat.xml
similarity index 97%
rename from tools/new_operations/concat.xml
rename to tools/new_operations/gops_concat_1/1.0.0/concat.xml
index e859117522d..010bb5d6c85 100644
--- a/tools/new_operations/concat.xml
+++ b/tools/new_operations/gops_concat_1/1.0.0/concat.xml
@@ -14,7 +14,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_concat.py b/tools/new_operations/gops_concat_1/1.0.0/gops_concat.py
similarity index 98%
rename from tools/new_operations/gops_concat.py
rename to tools/new_operations/gops_concat_1/1.0.0/gops_concat.py
index 62f5c41143e..982791f7051 100644
--- a/tools/new_operations/gops_concat.py
+++ b/tools/new_operations/gops_concat_1/1.0.0/gops_concat.py
@@ -27,7 +27,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.concat import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/coverage.xml b/tools/new_operations/gops_coverage_1/1.0.0/coverage.xml
similarity index 98%
rename from tools/new_operations/coverage.xml
rename to tools/new_operations/gops_coverage_1/1.0.0/coverage.xml
index 3c72c99c357..420b4d99b8d 100644
--- a/tools/new_operations/coverage.xml
+++ b/tools/new_operations/gops_coverage_1/1.0.0/coverage.xml
@@ -12,7 +12,7 @@
   <outputs>
     <data format="interval" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_coverage.py b/tools/new_operations/gops_coverage_1/1.0.0/gops_coverage.py
similarity index 98%
rename from tools/new_operations/gops_coverage.py
rename to tools/new_operations/gops_coverage_1/1.0.0/gops_coverage.py
index 615e2c4e4fa..32e8df50c67 100644
--- a/tools/new_operations/gops_coverage.py
+++ b/tools/new_operations/gops_coverage_1/1.0.0/gops_coverage.py
@@ -22,7 +22,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.coverage import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/gops_intersect.py b/tools/new_operations/gops_intersect_1/1.0.0/gops_intersect.py
similarity index 98%
rename from tools/new_operations/gops_intersect.py
rename to tools/new_operations/gops_intersect_1/1.0.0/gops_intersect.py
index cc0fb66f741..467b4759a45 100755
--- a/tools/new_operations/gops_intersect.py
+++ b/tools/new_operations/gops_intersect_1/1.0.0/gops_intersect.py
@@ -23,7 +23,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.intersect import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/gops_intersect_1/1.0.0/intersect.xml
similarity index 96%
rename from tools/new_operations/intersect.xml
rename to tools/new_operations/gops_intersect_1/1.0.0/intersect.xml
index 4a012f03443..ad71c779b5c 100644
--- a/tools/new_operations/intersect.xml
+++ b/tools/new_operations/gops_intersect_1/1.0.0/intersect.xml
@@ -20,7 +20,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_join.py b/tools/new_operations/gops_join_1/1.0.0/gops_join.py
similarity index 98%
rename from tools/new_operations/gops_join.py
rename to tools/new_operations/gops_join_1/1.0.0/gops_join.py
index 08fb86bb0b6..9ae87bebe0b 100644
--- a/tools/new_operations/gops_join.py
+++ b/tools/new_operations/gops_join_1/1.0.0/gops_join.py
@@ -22,7 +22,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.join import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/join.xml b/tools/new_operations/gops_join_1/1.0.0/join.xml
similarity index 99%
rename from tools/new_operations/join.xml
rename to tools/new_operations/gops_join_1/1.0.0/join.xml
index c801b20ca7e..e54a9884bb0 100644
--- a/tools/new_operations/join.xml
+++ b/tools/new_operations/gops_join_1/1.0.0/join.xml
@@ -21,7 +21,7 @@
   <outputs>
     <data format="interval" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/gops_merge.py b/tools/new_operations/gops_merge_1/1.0.0/gops_merge.py
similarity index 98%
rename from tools/new_operations/gops_merge.py
rename to tools/new_operations/gops_merge_1/1.0.0/gops_merge.py
index 3c2c9917da7..c056d4f9382 100644
--- a/tools/new_operations/gops_merge.py
+++ b/tools/new_operations/gops_merge_1/1.0.0/gops_merge.py
@@ -22,7 +22,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.merge import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/merge.xml b/tools/new_operations/gops_merge_1/1.0.0/merge.xml
similarity index 97%
rename from tools/new_operations/merge.xml
rename to tools/new_operations/gops_merge_1/1.0.0/merge.xml
index b842d10ecfd..918fd1779f4 100644
--- a/tools/new_operations/merge.xml
+++ b/tools/new_operations/gops_merge_1/1.0.0/merge.xml
@@ -12,7 +12,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py">
+  <code file="../../operation_filter.py">
     <hook exec_after_process="exec_after_merge" />
   </code>
   <tests>
diff --git a/tools/new_operations/gops_subtract.py b/tools/new_operations/gops_subtract_1/1.0.0/gops_subtract.py
similarity index 98%
rename from tools/new_operations/gops_subtract.py
rename to tools/new_operations/gops_subtract_1/1.0.0/gops_subtract.py
index 4cbc1e84eec..d8a53070a5a 100644
--- a/tools/new_operations/gops_subtract.py
+++ b/tools/new_operations/gops_subtract_1/1.0.0/gops_subtract.py
@@ -24,7 +24,7 @@ from bx.intervals.io import *
 from bx.intervals.operations.subtract import *
 from bx.cookbook import doc_optparse
 
-from galaxyops import *
+from galaxy.tools.util.galaxyops import *
 
 def main():
 
diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/gops_subtract_1/1.0.0/subtract.xml
similarity index 98%
rename from tools/new_operations/subtract.xml
rename to tools/new_operations/gops_subtract_1/1.0.0/subtract.xml
index dd12648738c..9af4649e212 100644
--- a/tools/new_operations/subtract.xml
+++ b/tools/new_operations/gops_subtract_1/1.0.0/subtract.xml
@@ -23,7 +23,7 @@
   <outputs>
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
-  <code file="operation_filter.py"/>
+  <code file="../../operation_filter.py"/>
   <tests>
     <test>
       <param name="input1" value="1.bed" />
diff --git a/tools/new_operations/subtract_query.py b/tools/new_operations/subtract_query1/1.0.0/subtract_query.py
similarity index 100%
rename from tools/new_operations/subtract_query.py
rename to tools/new_operations/subtract_query1/1.0.0/subtract_query.py
diff --git a/tools/new_operations/subtract_query.xml b/tools/new_operations/subtract_query1/1.0.0/subtract_query.xml
similarity index 100%
rename from tools/new_operations/subtract_query.xml
rename to tools/new_operations/subtract_query1/1.0.0/subtract_query.xml