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comparison rank_terms.xml @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 95a05c1ef5d5
children a631c2f6d913
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_rank_terms" name="Rank Terms" version="1.0.0"> 1 <tool id="gd_rank_terms" name="Rank Terms" version="1.1.0">
2 <description>: Assess the enrichment/depletion of a gene set for GO terms</description> 2 <description>: Assess the enrichment/depletion of a gene set for GO terms</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 #set $t_col1_0 = int(str($t_col1)) - 1 5 #set $t_col1_0 = int(str($t_col1)) - 1
6 #set $t_col2_0 = int(str($t_col2)) - 1 6 #set $t_col2_0 = int(str($t_col2)) - 1
7 #set $g_col2_0 = int(str($g_col2)) - 1 7 #set $g_col2_0 = int(str($g_col2)) - 1
8 rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --output "$output" 8 rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --statsTest "$stat" --output "$output"
9 </command> 9 </command>
10 10
11 <inputs> 11 <inputs>
12 <param name="input1" type="data" format="tabular" label="Query dataset" /> 12 <param name="input1" type="data" format="tabular" label="Query dataset" />
13 <param name="t_col1" type="data_column" data_ref="input1" label="Column with ENSEMBL transcript codes" /> 13 <param name="t_col1" type="data_column" data_ref="input1" label="Column with ENSEMBL transcript codes" />
14
15 <param name="input2" type="data" format="tabular" label="Background dataset" /> 14 <param name="input2" type="data" format="tabular" label="Background dataset" />
16 <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" /> 15 <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" />
17 <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" /> 16 <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" />
17 <param name="stat" type="select" label="Statistic for determining enrichment/depletion">
18 <option value="fisher" selected="true">two-tailed Fisher's exact test</option>
19 <option value="hypergeometric">hypergeometric test</option>
20 <option value="binomial">binomial probability</option>
21 </param>
18 </inputs> 22 </inputs>
19 23
20 <outputs> 24 <outputs>
21 <data name="output" format="tabular" /> 25 <data name="output" format="tabular" />
22 </outputs> 26 </outputs>
39 ----- 43 -----
40 44
41 **What it does** 45 **What it does**
42 46
43 Given a query set of genes from a larger background dataset, this tool 47 Given a query set of genes from a larger background dataset, this tool
44 evaluates the statistical over- or under-representation of Gene Ontology 48 evaluates the over- or under-representation of Gene Ontology terms in the
45 terms in the query set, using a two-tailed Fisher's exact test. 49 query set, using the specified statistical test.
46 50
47 The output contains a row for each GO term, with the following columns: 51 The output contains a row for each GO term, with the following columns:
48 52
49 1. count: the number of genes in the query set that are in this GO category 53 1. count: the number of genes in the query set that are in this GO category
50 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set 54 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set
51 3. ranking of this term, based on its representation ("1" is highest) 55 3. ranking of this term, based on its representation ("1" is highest)
52 4. Fisher probability of enrichment/depletion of this GO category in the query dataset 56 4. probability of depletion of this GO category in the query dataset
53 5. GO term 57 5. probability of enrichment of this GO category in the query dataset
58 6. GO term
54 59
55 </help> 60 </help>
56 </tool> 61 </tool>