Mercurial > repos > miller-lab > genome_diversity
comparison rank_pathways.xml @ 14:8ae67e9fb6ff
Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
| author | miller-lab |
|---|---|
| date | Fri, 28 Sep 2012 11:35:56 -0400 |
| parents | |
| children | d6b961721037 |
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| 13:fdb4240fb565 | 14:8ae67e9fb6ff |
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| 1 <tool id="gd_calc_freq" name="Rank Pathways" version="1.0.0"> | |
| 2 <description>: Assess the impact of gene sets on pathways</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 #if str($output_format) == 'a' | |
| 6 calctfreq.py | |
| 7 #else if str($output_format) == 'b' | |
| 8 calclenchange.py | |
| 9 #end if | |
| 10 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.rank.loc" | |
| 11 "--species=${input.metadata.dbkey}" | |
| 12 "--input=${input}" | |
| 13 "--output=${output}" | |
| 14 "--posKEGGclmn=${input.metadata.kegg_path}" | |
| 15 "--KEGGgeneposcolmn=${input.metadata.kegg_gene}" | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="input" type="data" format="gd_sap" label="Table"> | |
| 20 <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" /> | |
| 21 </param> | |
| 22 <param name="output_format" type="select" label="Output format"> | |
| 23 <option value="a" selected="true">ranked by percentage of genes affected</option> | |
| 24 <option value="b">ranked by change in length and number of paths</option> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 | |
| 28 <outputs> | |
| 29 <data name="output" format="tabular" /> | |
| 30 </outputs> | |
| 31 | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" /> | |
| 35 <param name="output_format" value="a" /> | |
| 36 <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" /> | |
| 37 </test> | |
| 38 </tests> | |
| 39 | |
| 40 <help> | |
| 41 | |
| 42 **What it does** | |
| 43 | |
| 44 This tool produces a table ranking the pathways based on the percentage | |
| 45 of genes in an input dataset, out of the total in each pathway. | |
| 46 Alternatively, the tool ranks the pathways based on the change in | |
| 47 length and number of paths connecting sources and sinks. This change is | |
| 48 calculated between graphs representing pathways with and without excluding | |
| 49 the nodes that represent the genes in an input list. Sources are all | |
| 50 the nodes representing the initial reactants/products in the pathway. | |
| 51 Sinks are all the nodes representing the final reactants/products in | |
| 52 the pathway. | |
| 53 | |
| 54 If pathways are ranked by percentage of genes affected, the output is | |
| 55 a tabular dataset with the following columns: | |
| 56 | |
| 57 1. number of genes in the pathway present in the input dataset | |
| 58 2. percentage of the total genes in the pathway included in the input dataset | |
| 59 3. rank of the frequency (from high freq to low freq) | |
| 60 4. name of the pathway | |
| 61 | |
| 62 If pathways are ranked by change in length and number of paths, the | |
| 63 output is a tabular dataset with the following columns: | |
| 64 | |
| 65 1. change in the mean length of paths between sources and sinks | |
| 66 2. mean length of paths between sources and sinks in the pathway including the genes in the input dataset. If the pathway do not have sources/sinks, the length is assumed to be infinite (I) | |
| 67 3. mean length of paths between sources and sinks in the pathway excluding the genes in the input dataset. If the pathway do not have sources/sinks, the length is assumed to be infinite (I) | |
| 68 4. rank of the change in the mean length of paths between sources and sinks (from high change to low change) | |
| 69 5. change in the number of paths between sources and sinks | |
| 70 6. number of paths between sources and sinks in the pathway including the genes in the input dataset. If the pathway do not have sources/sinks, it is assumed to be a circuit (C) | |
| 71 7. number of paths between sources and sinks in the pathway excluding the genes in the input dataset. If the pathway do not have sources/sinks, it is assumed to be a circuit (C) | |
| 72 8. rank of the change in the number of paths between sources and sinks (from high change to low change) | |
| 73 9. name of the pathway | |
| 74 | |
| 75 </help> | |
| 76 </tool> |