# HG changeset patch
# User devteam
# Date 1498171969 14400
# Node ID 381cd27bf67a893084a9ad2ce1645bc2a38fa417
# Parent 0926c81f382ce7c4bad209e937f44118e5529cdc
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
diff -r 0926c81f382c -r 381cd27bf67a gops_merge.py
--- a/gops_merge.py Wed Nov 11 12:49:11 2015 -0500
+++ b/gops_merge.py Thu Jun 22 18:52:49 2017 -0400
@@ -1,17 +1,20 @@
#!/usr/bin/env python
"""
-Merge overlaping regions.
+Merge overlapping regions.
usage: %prog in_file out_file
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
-m, --mincols=N: Require this much overlap (default 1bp)
-3, --threecol: Output 3 column bed
"""
+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.merge import merge
-from bx.cookbook import doc_optparse
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
@@ -55,14 +58,15 @@
out_file.write( "%s\n" % "\t".join( line ) )
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 __name__ == "__main__":
main()
diff -r 0926c81f382c -r 381cd27bf67a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jun 22 18:52:49 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 0926c81f382c -r 381cd27bf67a merge.xml
--- a/merge.xml Wed Nov 11 12:49:11 2015 -0500
+++ b/merge.xml Thu Jun 22 18:52:49 2017 -0400
@@ -1,62 +1,54 @@
- the overlapping intervals of a dataset
-
- bx-python
- galaxy-ops
-
- gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype
-
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+ the overlapping intervals of a dataset
+
+ macros.xml
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-
\ No newline at end of file
+ ]]>
+
diff -r 0926c81f382c -r 381cd27bf67a operation_filter.py
--- a/operation_filter.py Wed Nov 11 12:49:11 2015 -0500
+++ b/operation_filter.py Thu Jun 22 18:52:49 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 0926c81f382c -r 381cd27bf67a tool_dependencies.xml
--- a/tool_dependencies.xml Wed Nov 11 12:49:11 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-
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-