Mercurial > repos > miller-lab > genome_diversity
comparison 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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| 21:d6b961721037 | 22:95a05c1ef5d5 |
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| 1 <tool id="gd_calc_freq" name="Rank Pathways" version="1.0.0"> | 1 <tool id="gd_calc_freq" name="Rank Pathways" version="1.1.0"> |
| 2 <description>: Assess the impact of gene sets on pathways</description> | 2 <description>: Assess the impact of a gene set on KEGG pathways</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 #if str($output_format) == 'a' | 5 #if str($output_format) == 'a' |
| 6 calctfreq.py | 6 rank_pathways_pct.py |
| 7 #else if str($output_format) == 'b' | 7 #else if str($output_format) == 'b' |
| 8 calclenchange.py | 8 calclenchange.py |
| 9 #end if | 9 #end if |
| 10 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.rank.loc" | 10 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.rank.loc" |
| 11 "--species=${input.metadata.dbkey}" | 11 "--species=${input.metadata.dbkey}" |
| 69 a tabular dataset with the following columns: | 69 a tabular dataset with the following columns: |
| 70 | 70 |
| 71 1. number of genes in the pathway present in the input dataset | 71 1. number of genes in the pathway present in the input dataset |
| 72 2. percentage of the total genes in the pathway included in the input dataset | 72 2. percentage of the total genes in the pathway included in the input dataset |
| 73 3. rank of the frequency (from high freq to low freq) | 73 3. rank of the frequency (from high freq to low freq) |
| 74 4. name of the pathway | 74 4. Fisher probability of enrichment/depletion of pathway genes in the input dataset |
| 75 5. name of the pathway | |
| 75 | 76 |
| 76 If pathways are ranked by change in length and number of paths, the | 77 If pathways are ranked by change in length and number of paths, the |
| 77 output is a tabular dataset with the following columns: | 78 output is a tabular dataset with the following columns: |
| 78 | 79 |
| 79 1. change in the mean length of paths between sources and sinks | 80 1. change in the mean length of paths between sources and sinks |