Added tool version directories to new_operations tools directory.

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" />

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" />

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 )

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" />

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():
 

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>

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

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" />

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

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" />

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():
 

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" />

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():
 

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():
 

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" />

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():
 

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" />

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():
 

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>

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():
 

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" />