diff rank_terms.xml @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

--- a/rank_terms.xml	Mon Jun 03 12:29:29 2013 -0400
+++ b/rank_terms.xml	Mon Jul 15 10:47:35 2013 -0400
@@ -1,20 +1,24 @@
-<tool id="gd_rank_terms" name="Rank Terms" version="1.0.0">
+<tool id="gd_rank_terms" name="Rank Terms" version="1.1.0">
   <description>: Assess the enrichment/depletion of a gene set for GO terms</description>
 
   <command interpreter="python">
     #set $t_col1_0 = int(str($t_col1)) - 1
     #set $t_col2_0 = int(str($t_col2)) - 1
     #set $g_col2_0 = int(str($g_col2)) - 1
-    rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --output "$output"
+    rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --statsTest "$stat" --output "$output"
   </command>
 
   <inputs>
     <param name="input1" type="data" format="tabular" label="Query dataset" />
     <param name="t_col1" type="data_column" data_ref="input1" label="Column with ENSEMBL transcript codes" />
-
     <param name="input2" type="data" format="tabular" label="Background dataset" />
     <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" />
     <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" />
+    <param name="stat" type="select" label="Statistic for determining enrichment/depletion">
+      <option value="fisher" selected="true">two-tailed Fisher's exact test</option>
+      <option value="hypergeometric">hypergeometric test</option>
+      <option value="binomial">binomial probability</option>
+    </param>
   </inputs>
 
   <outputs>
@@ -41,16 +45,17 @@
 **What it does**
 
 Given a query set of genes from a larger background dataset, this tool
-evaluates the statistical over- or under-representation of Gene Ontology
-terms in the query set, using a two-tailed Fisher's exact test.
+evaluates the over- or under-representation of Gene Ontology terms in the
+query set, using the specified statistical test.
 
 The output contains a row for each GO term, with the following columns:
 
 1. count: the number of genes in the query set that are in this GO category
 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set
 3. ranking of this term, based on its representation ("1" is highest)
-4. Fisher probability of enrichment/depletion of this GO category in the query dataset
-5. GO term
+4. probability of depletion of this GO category in the query dataset
+5. probability of enrichment of this GO category in the query dataset
+6. GO term
 
   </help>
 </tool>