Mercurial > repos > miller-lab > genome_diversity
diff rank_pathways.xml @ 22:95a05c1ef5d5
update to devshed revision aaece207bd01
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Mon, 11 Mar 2013 11:28:06 -0400 |
| parents | d6b961721037 |
| children | 8997f2ca8c7a |
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--- a/rank_pathways.xml Mon Nov 05 12:44:17 2012 -0500 +++ b/rank_pathways.xml Mon Mar 11 11:28:06 2013 -0400 @@ -1,9 +1,9 @@ -<tool id="gd_calc_freq" name="Rank Pathways" version="1.0.0"> - <description>: Assess the impact of gene sets on pathways</description> +<tool id="gd_calc_freq" name="Rank Pathways" version="1.1.0"> + <description>: Assess the impact of a gene set on KEGG pathways</description> <command interpreter="python"> #if str($output_format) == 'a' - calctfreq.py + rank_pathways_pct.py #else if str($output_format) == 'b' calclenchange.py #end if @@ -71,7 +71,8 @@ 1. number of genes in the pathway present in the input dataset 2. percentage of the total genes in the pathway included in the input dataset 3. rank of the frequency (from high freq to low freq) -4. name of the pathway +4. Fisher probability of enrichment/depletion of pathway genes in the input dataset +5. name of the pathway If pathways are ranked by change in length and number of paths, the output is a tabular dataset with the following columns: