Mercurial > repos > devteam > count_gff_features

changeset 1:188392a0d0a8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features commit d242cab2b4e86bc8a16eeaee7e5dc0264e617170
author devteam
date Tue, 06 Jun 2017 18:37:53 -0400
parents fabda887a71f
children
files count_gff_features.py count_gff_features.xml tool_dependencies.xml
diffstat 3 files changed, 13 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/count_gff_features.py	Mon Jul 28 11:56:10 2014 -0400
+++ b/count_gff_features.py	Tue Jun 06 18:37:53 2017 -0400
@@ -1,10 +1,13 @@
 #!/usr/bin/env python
 # This tool takes a gff file as input and counts the number of features in it.
 
-import sys, fileinput
-from galaxy import eggs
+from __future__ import print_function
+
+import fileinput
+import sys
+
+from bx.intervals.io import GenomicInterval
 from galaxy.datatypes.util.gff_util import GFFReaderWrapper
-from bx.intervals.io import GenomicInterval
 
 # Get args.
 input_file = sys.argv[1:]
@@ -15,4 +18,4 @@
     if isinstance( feature, GenomicInterval ):
         count += 1
 
-print count
\ No newline at end of file
+print(count)
--- a/count_gff_features.xml	Mon Jul 28 11:56:10 2014 -0400
+++ b/count_gff_features.xml	Tue Jun 06 18:37:53 2017 -0400
@@ -1,10 +1,12 @@
-<tool id="count_gff_features" name="Count GFF Features" version="0.1">
+<tool id="count_gff_features" name="Count GFF Features" version="0.2">
     <description></description>
     <requirements>
-        <requirement type="package" version="0.7.1">bx-python</requirement>
+        <requirement type="package" version="1.1.0">galaxy-ops</requirement>
     </requirements>
-    <command interpreter="python">
-        count_gff_features.py $input &gt; $output
+    <command><![CDATA[
+        python '$__tool_directory__/count_gff_features.py'
+            '$input' > '$output'
+    ]]>
     </command>
     <inputs>
         <param format="gff" name="input" type="data" label="GFF Dataset to Filter"/>
--- a/tool_dependencies.xml	Mon Jul 28 11:56:10 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bx-python" version="0.7.1">
-      <repository changeset_revision="2d0c08728bca" name="package_bx_python_0_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>