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annotate rank_terms.xml @ 26:91e835060ad2

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Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
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1 <tool id="gd_rank_terms" name="Rank Terms" version="1.0.0">
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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 $g_col2_0 --output "$output"
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9 </command>
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10
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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
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15 <param name="input2" type="data" format="tabular" label="Background dataset" />
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16 <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" />
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17 <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" />
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18 </inputs>
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19
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20 <outputs>
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21 <data name="output" format="tabular" />
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22 </outputs>
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23
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24 <help>
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25
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26 **Dataset formats**
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27
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28 All of the input and output datasets are in tabular_ format.
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29 The query dataset has a column containing ENSEMBL transcript codes for
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30 the gene set of interest, while the background dataset has one column
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31 with ENSEMBL transcript codes and another with GO terms, for some
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32 larger universe of genes.
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33 The output dataset is described below.
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34 (`Dataset missing?`_)
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35
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36 .. _tabular: ./static/formatHelp.html#tab
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37 .. _Dataset missing?: ./static/formatHelp.html
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38
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39 -----
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40
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41 **What it does**
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42
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43 Given a query set of genes from a larger background dataset, this tool
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44 evaluates the statistical over- or under-representation of Gene Ontology
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45 terms in the query set, using a two-tailed Fisher's exact test.
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46
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47 The output contains a row for each GO term, with the following columns:
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48
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49 1. count: the number of genes in the query set that are in this GO category
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50 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set
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51 3. ranking of this term, based on its representation ("1" is highest)
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52 4. Fisher probability of enrichment/depletion of this GO category in the query dataset
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53 5. GO term
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54
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55 </help>
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56 </tool>