# HG changeset patch # User devteam # Date 1498171956 14400 # Node ID a10f49d9218a85165ca62866208157b9e8b2cd77 # Parent ffbd1de29c282ef948b1b356eebbaacf00f60b59 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 diff -r ffbd1de29c28 -r a10f49d9218a gops_join.py --- a/gops_join.py Wed Nov 11 12:48:58 2015 -0500 +++ b/gops_join.py Thu Jun 22 18:52:36 2017 -0400 @@ -8,11 +8,14 @@ -m, --mincols=N: Require this much overlap (default 1bp) -f, --fill=N: none, right, left, both """ +from __future__ import print_function + import fileinput import sys + +from bx.cookbook import doc_optparse from bx.intervals.io import NiceReaderWrapper from bx.intervals.operations.join import join -from bx.cookbook import doc_optparse from bx.tabular.io import ParseError from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped @@ -61,7 +64,7 @@ out_file.write( "%s\n" % "\t".join( outfields ) ) else: out_file.write( "%s\n" % outfields ) - except ParseError, exc: + except ParseError as exc: out_file.close() fail( "Invalid file format: %s" % str( exc ) ) except MemoryError: @@ -71,9 +74,10 @@ out_file.close() if g1.skipped > 0: - print skipped( g1, filedesc=" of 1st dataset" ) + print(skipped( g1, filedesc=" of 1st dataset" )) if g2.skipped > 0: - print skipped( g2, filedesc=" of 2nd dataset" ) + print(skipped( g2, filedesc=" of 2nd dataset" )) + if __name__ == "__main__": main() diff -r ffbd1de29c28 -r a10f49d9218a join.xml --- a/join.xml Wed Nov 11 12:48:58 2015 -0500 +++ b/join.xml Thu Jun 22 18:52:36 2017 -0400 @@ -1,98 +1,92 @@ - the intervals of two datasets side-by-side - - bx-python - galaxy-ops - - gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill - - - Join - - - with - - - with min overlap - - - - - - - - - - - -


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+    the intervals of two datasets side-by-side
+    
+        macros.xml
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+    ]]>


diff -r ffbd1de29c28 -r a10f49d9218a macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:52:36 2017 -0400
@@ -0,0 +1,20 @@
+
+
+    
+        
+            bx-python
+            galaxy-ops
+        
+    
+    
+-----
+
+**Screencasts!**
+
+See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
+
+.. _Screencasts: https://galaxyproject.org/learn/interval-operations/
+
+-----
+    
+
diff -r ffbd1de29c28 -r a10f49d9218a operation_filter.py
--- a/operation_filter.py	Wed Nov 11 12:48:58 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:52:36 2017 -0400
@@ -1,8 +1,7 @@
 # runs after the job (and after the default post-filter)
+from galaxy.jobs.handler import JOB_ERROR
 from galaxy.tools.parameters import DataToolParameter
 
-from galaxy.jobs.handler import JOB_ERROR
-
 # Older py compatibility
 try:
     set()
@@ -14,7 +13,7 @@
     dbkeys = set()
     data_param_names = set()
     data_params = 0
-    for name, param in page_param_map.iteritems():
+    for name, param in page_param_map.items():
         if isinstance( param, DataToolParameter ):
             # for each dataset parameter
             if param_values.get(name, None) is not None:
@@ -53,7 +52,6 @@
         try:
             if stderr and len( stderr ) > 0:
                 raise Exception( stderr )
-
         except Exception:
             data.blurb = JOB_ERROR
             data.state = JOB_ERROR
diff -r ffbd1de29c28 -r a10f49d9218a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:48:58 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
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