1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e7873feacc48/ changeset: r5363:e7873feacc48 user: jgoecks date: 2011-04-11 15:39:55 summary: Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well. affected #: 12 files (140 bytes) --- a/tool_conf.xml.main Fri Apr 08 17:07:08 2011 -0400 +++ b/tool_conf.xml.main Mon Apr 11 09:39:55 2011 -0400 @@ -78,6 +78,7 @@ <tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" /> + <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section><section name="Join, Subtract and Group" id="group"><tool file="filters/joiner.xml" /> --- a/tool_conf.xml.sample Fri Apr 08 17:07:08 2011 -0400 +++ b/tool_conf.xml.sample Mon Apr 11 09:39:55 2011 -0400 @@ -67,6 +67,7 @@ <tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" /> + <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section><section name="Join, Subtract and Group" id="group"><tool file="filters/joiner.xml" /> --- a/tools/filters/gff/extract_GFF_Features.xml Fri Apr 08 17:07:08 2011 -0400 +++ b/tools/filters/gff/extract_GFF_Features.xml Mon Apr 11 09:39:55 2011 -0400 @@ -1,5 +1,5 @@ <tool id="Extract_features1" name="Extract features"> - <description> from GFF file</description> + <description> from GFF data</description><command interpreter="python">extract_GFF_Features.py $input1 $out_file1 ${column_choice.col} ${column_choice.feature}</command><inputs><param format="gff" name="input1" type="data" label="Select GFF data"/> --- a/tools/filters/gff/gff_filter_by_attribute.xml Fri Apr 08 17:07:08 2011 -0400 +++ b/tools/filters/gff/gff_filter_by_attribute.xml Mon Apr 11 09:39:55 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="gff_filter_by_attribute" name="Filter GFF file by attribute" version="0.1"> +<tool id="gff_filter_by_attribute" name="Filter GFF data by attribute" version="0.1"><description>using simple expressions</description><command interpreter="python"> gff_filter_by_attribute.py $input $out_file1 "$attribute_type" "$attribute_name" "$cond" --- a/tools/filters/gff/gff_filter_by_feature_count.xml Fri Apr 08 17:07:08 2011 -0400 +++ b/tools/filters/gff/gff_filter_by_feature_count.xml Mon Apr 11 09:39:55 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="gff_filter_by_feature_count" name="Filter GFF file by feature count" version="0.1"> +<tool id="gff_filter_by_feature_count" name="Filter GFF data by feature count" version="0.1"><description>using simple expressions</description><command interpreter="python"> gff_filter_by_feature_count.py $input_file1 $out_file1 "$feature_name" "$cond" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.