# HG changeset patch
# User caleb-easterly
# Date 1506378063 14400
# Node ID ebc00346c9eb08dc9a02f9c966a44cdafb3a2c3a

planemo upload commit b5afbd13a9ecfc706597cd93681eb5c1be3145e9-dirty

diff -r 000000000000 -r ebc00346c9eb README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Mon Sep 25 18:21:03 2017 -0400
@@ -0,0 +1,1 @@
+tool to prepare data for REVIGO
diff -r 000000000000 -r ebc00346c9eb revigoWrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/revigoWrapper.xml	Mon Sep 25 18:21:03 2017 -0400
@@ -0,0 +1,74 @@
+<tool id="revigo-data-prep" name="Prepare Data for REVIGO" version="0.1">
+    <description>Cut columns from tabular data and define as REVIGO datatype.</description>
+    <command>
+    #if ($include_numeric.include_numeric_column == "yes"):
+         awk 
+            '{ print \$goTermsCol"\t"\$numberCol}'
+            goTermsCol=$goTermsCol
+            numberCol=$include_numeric.numberCol
+            $input > $out_file1
+    #else  
+        awk '{ print \$goTermsCol}' 
+            goTermsCol=$goTermsCol 
+            $input > $out_file1
+    #end if
+    </command>
+    <inputs>
+        <param format="tabular" name="input" type="data" label="Input Dataset" />
+        <param name="goTermsCol"
+            type="data_column"
+            data_ref="input"
+            value="1"
+            accept_default="true"
+            label="Select Column of GO Terms" />
+        <conditional name="include_numeric">
+            <param name="include_numeric_column" type="select" label="Include measures of enrichment?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param name="numberCol" 
+                    type="data_column" 
+                    data_ref="input"
+                    value="2" 
+                    accept_default="true" 
+                    label="Select Column of p-values, etc." />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="revigo" 
+            name="out_file1" 
+            metadata_source="input" 
+            label="Prepare ${on_string} for REVIGO"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test.tab" ftype="tabular" />
+            <param name="goTermsCol" value="1"/>
+            <param name="include_numeric_column" value="yes"/>
+            <param name="numberCol" value="3"/>
+            <output name="out_file1" file="test1.out" ftype="revigo"/>
+        </test>
+        <test>
+            <param name="input" value="test.tab" ftype="tabular" />
+            <param name="goTermsCol" value="1"/>
+            <param name="include_numeric_column" value="no"/>
+            <output name="out_file1" file="test2.out" ftype="revigo"/>
+        </test>
+    </tests>
+    <help>
+Prepare data for REVIGO
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{REVIGOtool,
+            author = {Caleb Easterly},
+            date = {22 Sept 2017},
+            title = {REVIGO Data Prep Tool}
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r ebc00346c9eb test-data/test.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tab	Mon Sep 25 18:21:03 2017 -0400
@@ -0,0 +1,2 @@
+GO:123	blah	0.001	otherdata
+GO:456	blah	0.002	other
diff -r 000000000000 -r ebc00346c9eb test-data/test1.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.out	Mon Sep 25 18:21:03 2017 -0400
@@ -0,0 +1,2 @@
+GO:123	0.001
+GO:456	0.002
diff -r 000000000000 -r ebc00346c9eb test-data/test2.out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.out	Mon Sep 25 18:21:03 2017 -0400
@@ -0,0 +1,2 @@
+GO:123
+GO:456