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annotate rank_terms.xml @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
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1 <tool id="gd_rank_terms" name="Rank Terms" version="1.1.0">
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2 <description>: Assess the enrichment/depletion of a gene set for GO terms</description>
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3
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4 <command interpreter="python">
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5 #set $t_col1_0 = int(str($t_col1)) - 1
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6 #set $t_col2_0 = int(str($t_col2)) - 1
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7 #set $g_col2_0 = int(str($g_col2)) - 1
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8 rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --statsTest "$stat" --output "$output"
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9 </command>
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11 <inputs>
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12 <param name="input1" type="data" format="tabular" label="Query dataset" />
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13 <param name="t_col1" type="data_column" data_ref="input1" label="Column with ENSEMBL transcript codes" />
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14 <param name="input2" type="data" format="tabular" label="Background dataset" />
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15 <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" />
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16 <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" />
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17 <param name="stat" type="select" label="Statistic for determining enrichment/depletion">
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18 <option value="fisher" selected="true">two-tailed Fisher's exact test</option>
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19 <option value="hypergeometric">hypergeometric test</option>
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20 <option value="binomial">binomial probability</option>
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21 </param>
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22 </inputs>
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24 <outputs>
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25 <data name="output" format="tabular" />
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26 </outputs>
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28 <requirements>
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29 <requirement type="package" version="0.1.4">fisher</requirement>
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30 </requirements>
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31
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32 <help>
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33
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34 **Dataset formats**
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35
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36 All of the input and output datasets are in tabular_ format.
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37 The query dataset has a column containing ENSEMBL transcript codes for
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38 the gene set of interest, while the background dataset has one column
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39 with ENSEMBL transcript codes and another with GO terms, for some
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40 larger universe of genes.
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41 The output dataset is described below.
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42 (`Dataset missing?`_)
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44 .. _tabular: ./static/formatHelp.html#tab
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45 .. _Dataset missing?: ./static/formatHelp.html
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47 -----
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48
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49 **What it does**
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50
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51 Given a query set of genes from a larger background dataset, this tool
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52 evaluates the over- or under-representation of Gene Ontology terms in the
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53 query set, using the specified statistical test.
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55 The output contains a row for each GO term, with the following columns:
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57 1. count: the number of genes in the query set that are in this GO category
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58 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set
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59 3. ranking of this term, based on its representation ("1" is highest)
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60 4. probability of depletion of this GO category in the query dataset
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61 5. probability of enrichment of this GO category in the query dataset
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62 6. GO term
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63
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64 </help>
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65 </tool>