# HG changeset patch # User devteam # Date 1498171246 14400 # Node ID 32e1c8dac438d825df6aeaf487a9374ad7a6b5f8 # Parent d491589307e7d925652de3f24b20091a5cb0baac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689 diff -r d491589307e7 -r 32e1c8dac438 concat.xml --- a/concat.xml Wed Nov 11 12:47:51 2015 -0500 +++ b/concat.xml Thu Jun 22 18:40:46 2017 -0400 @@ -1,53 +1,47 @@ - two datasets into one dataset - - bx-python - galaxy-ops - - gops_concat.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} $sameformat - - - Concatenate - - - with - - - - - - - -


-  
-    
-      
-      
-      
-           
-    
-    
-      
-      
-      
-           
-       
-  
-  
-
+    two datasets into one dataset
+    
+        macros.xml
+    
+    
+    
+    
+    
+        
+        
+        
+    
+    
+        
+    
+    
+        
+            
+            
+            
+            
+        
+        
+            
+            
+            
+            
+        
+    
+     it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
 
------
-
-**Screencasts!**
-
-See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-
-.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-
------
+@SCREENCASTS@
 
 **Syntax**
 
@@ -58,6 +52,5 @@
 **Example**
 
 .. image:: gops_concatenate.gif
-
-
+    ]]>


diff -r d491589307e7 -r 32e1c8dac438 gops_concat.py
--- a/gops_concat.py	Wed Nov 11 12:47:51 2015 -0500
+++ b/gops_concat.py	Thu Jun 22 18:40:46 2017 -0400
@@ -12,12 +12,14 @@
     -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file
     -s, --sameformat: All files are precisely the same format.
 """
+from __future__ import print_function
 
 import fileinput
 import sys
+
+from bx.cookbook import doc_optparse
 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
 from bx.intervals.operations.concat import concat
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -59,16 +61,17 @@
                 out_file.write( "%s\n" % "\t".join( line.fields ) )
             else:
                 out_file.write( "%s\n" % line )
-    except ParseError, exc:
+    except ParseError as exc:
         out_file.close()
         fail( "Invalid file format: %s" % str( exc ) )
 
     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 d491589307e7 -r 32e1c8dac438 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:40:46 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 d491589307e7 -r 32e1c8dac438 operation_filter.py
--- a/operation_filter.py	Wed Nov 11 12:47:51 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:40:46 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 d491589307e7 -r 32e1c8dac438 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:47:51 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-  
-      
-    
-    
-      
-    
-