Mercurial > repos > devteam > count_gff_features
changeset 1:115bba486116 draft default tip
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 18:37:39 -0400 |
| parents | 002a1e6ef8d9 |
| children | |
| files | count_gff_features.py count_gff_features.xml tool_dependencies.xml |
| diffstat | 3 files changed, 13 insertions(+), 14 deletions(-) [+] |
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--- a/count_gff_features.py Mon Jul 28 11:30:20 2014 -0400 +++ b/count_gff_features.py Tue Jun 06 18:37:39 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 11:30:20 2014 -0400 +++ b/count_gff_features.xml Tue Jun 06 18:37:39 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 > $output + <command><![CDATA[ + python '$__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 11:30:20 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="35e2457234ef" name="package_bx_python_0_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>