changeset 5:dfbbc0291b36 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

--- a/gops_merge.py	Fri Dec 18 19:39:00 2015 -0500
+++ b/gops_merge.py	Thu Jun 22 18:51:08 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()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jun 22 18:51:08 2017 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.7.1">bx-python</requirement>
+            <requirement type="package" version="1.0.0">galaxy-ops</requirement>
+        </requirements>
+    </xml>
+    <token name="@SCREENCASTS@">
+-----
+
+**Screencasts!**
+
+See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
+
+.. _Screencasts: https://galaxyproject.org/learn/interval-operations/
+
+-----
+    </token>
+</macros>

--- a/merge.xml	Fri Dec 18 19:39:00 2015 -0500
+++ b/merge.xml	Thu Jun 22 18:51:08 2017 -0400
@@ -1,62 +1,54 @@
 <tool id="gops_merge_1" name="Merge" version="1.0.0">
-  <description>the overlapping intervals of a dataset</description>
-  <requirements>
-    <requirement type="package" version="0.7.1">bx-python</requirement>
-    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
-  </requirements>
-  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
-  <inputs>
-    <param format="interval" name="input1" type="data">
-      <label>Merge overlaping regions of</label>
-    </param>
-    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
-      <label>Output 3 column bed</label>
-    </param>
-   </inputs>
-  <outputs>
-    <data format="input" name="output" metadata_source="input1" />
-  </outputs>
-  <code file="operation_filter.py">
-    <hook exec_after_process="exec_after_merge" />
-  </code>
-  <tests>
-    <test>
-      <param name="input1" value="1.bed" />
-      <output name="output" file="gops-merge.dat" />
-      <param name="returntype" value="true" />
-    </test>
-    <test>
-      <param name="input1" value="2_mod.bed" ftype="interval"/>
-      <output name="output" file="gops_merge_diffCols.dat" />
-      <param name="returntype" value="true" />
-    </test>
-    <test>
-      <param name="input1" value="gops_bigint.interval" />
-      <output name="output" file="gops_merge_out2.bed" />
-      <param name="returntype" value="true" />
-    </test>
-  </tests>
-  <help>
-
+    <description>the overlapping intervals of a dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="operation_filter.py">
+        <hook exec_after_process="exec_after_merge" />
+    </code>
+    <command><![CDATA[
+python '$__tool_directory__/gops_merge.py'
+'$input1'
+'$output'
+-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
+$returntype
+    ]]></command>
+    <inputs>
+        <param name="input1" type="data" format="interval" label="Merge overlapping regions of" />
+        <param name="returntype" type="boolean" truevalue="-3" falsevalue="" label="Output 3 column bed" />
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input1" metadata_source="input1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="1.bed" />
+            <param name="returntype" value="true" />
+            <output name="output" file="gops-merge.dat" />
+        </test>
+        <test>
+            <param name="input1" value="2_mod.bed" ftype="interval"/>
+            <param name="returntype" value="true" />
+            <output name="output" file="gops_merge_diffCols.dat" />
+        </test>
+        <test>
+            <param name="input1" value="gops_bigint.interval" />
+            <param name="returntype" value="true" />
+            <output name="output" file="gops_merge_out2.bed" />
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: infomark
 
 **TIP:** If your dataset does not appear in the pulldown menu, it means that 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@
 
 This operation merges all overlapping intervals into single intervals.
 
 **Example**
 
 .. image:: gops_merge.gif
-
-</help>
-</tool>
\ No newline at end of file
+    ]]></help>
+</tool>

--- a/operation_filter.py	Fri Dec 18 19:39:00 2015 -0500
+++ b/operation_filter.py	Thu Jun 22 18:51:08 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

--- a/tool_dependencies.xml	Fri Dec 18 19:39:00 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository changeset_revision="35e2457234ef" name="package_bx_python_0_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="galaxy-ops" version="1.0.0">
-      <repository changeset_revision="60c9a7af1345" name="package_galaxy_ops_1_0_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>