# HG changeset patch # User devteam # Date 1498171206 14400 # Node ID 2cedec3759e49dae95d3e7ad15011f69de17bad0 # Parent 0a3e3133b09d2d9e5f51f7c0857f0500e7969a0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 diff -r 0a3e3133b09d -r 2cedec3759e4 basecoverage.xml --- a/basecoverage.xml Wed Nov 11 12:47:11 2015 -0500 +++ b/basecoverage.xml Thu Jun 22 18:40:06 2017 -0400 @@ -1,49 +1,43 @@ - of all intervals - gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} - - bx-python - galaxy-ops - - - - Compute coverage for - - - - - -


-  
-    
-      
-           
-    
-    
-      
-           
-    
-  
-  
-
+    of all intervals
+    
+        macros.xml
+    
+    
+    
+    
+    
+        
+    
+    
+        
+    
+    
+        
+            
+            
+        
+        
+            
+            
+        
+    
+    
+    ]]>


diff -r 0a3e3133b09d -r 2cedec3759e4 gops_basecoverage.py
--- a/gops_basecoverage.py	Wed Nov 11 12:47:11 2015 -0500
+++ b/gops_basecoverage.py	Thu Jun 22 18:40:06 2017 -0400
@@ -5,12 +5,14 @@
 usage: %prog in_file out_file
     -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
 """
+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.base_coverage import base_coverage
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -34,13 +36,14 @@
 
     try:
         bases = base_coverage(g1)
-    except ParseError, exc:
+    except ParseError as exc:
         fail( "Invalid file format: %s" % str( exc ) )
     out_file = open( out_fname, "w" )
     out_file.write( "%s\n" % str( bases ) )
     out_file.close()
     if g1.skipped > 0:
-        print skipped( g1, filedesc="" )
+        print(skipped( g1, filedesc="" ))
+
 
 if __name__ == "__main__":
     main()
diff -r 0a3e3133b09d -r 2cedec3759e4 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:40:06 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 0a3e3133b09d -r 2cedec3759e4 operation_filter.py
--- a/operation_filter.py	Wed Nov 11 12:47:11 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:40:06 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 0a3e3133b09d -r 2cedec3759e4 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:47:11 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-  
-      
-    
-    
-      
-    
-