# HG changeset patch
# User antmarge
# Date 1490830926 14400
# Node ID e29f18a2b212f86196dc58e2973207045e4d58c2
# Parent  21779cc1f7b62a80902c1d3551fa54338fe840bb
Uploaded

diff -r 21779cc1f7b6 -r e29f18a2b212 compGenes.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compGenes.xml	Wed Mar 29 19:42:06 2017 -0400
@@ -0,0 +1,53 @@
+<tool id="compGenes" name="Compare Genes" version="0.1.0">
+    
+    <!-- Margaret Antonio  17.01.08 -->
+
+    <description> compare gene aggregate fitness from two different experiments</description>
+    
+    <requirements>
+        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="2.45">perl_getopt_long</requirement>
+        <requirement type="package" version="1.02">perl_statistics_distributions</requiremnt>
+    </requirements>
+    
+    <command interpreter="perl">
+        compGenes.pl
+        -input1 $input1
+        -input2 $input2
+        -l1 $l1
+        -l2 $l2
+        -o $outfile
+    </command>
+   
+    <inputs>
+        <param name="input1" type="data" label="csv gene aggregate fitness file #1"/>
+        <param name="input2" type="data" label="csv gene aggregate fitness file #2"/>
+        <param name="l1" type="text" value ="input1" label="Label for input #1"/>
+        <param name="l2" type="text" value ="input2" label="Label for input #2"/>
+        
+
+    </inputs>
+   
+    <outputs>
+        <data format="csv" name="outfile"  />
+    </outputs>
+    
+    <help>
+        **What it does**
+        
+        This tool compares genes for an organism under different conditions. It takes two geneAgregate outputs and compares them calculating the difference in mean fitness for each gene. Example usage: compare organism in presence of control vs antibiotic. For different strains/genomes, where gene ids are not the same, use compStrains.pl;
+
+        
+        **The options explained**
+        
+        Input 1 and 2: These are the csv (comma separated values) files containing the gene fitness values. Since they should have been produced by the "Aggregate Fitness" tool, each line besides the header should represent the following information for a gene: Locus, Fitness, NumberofInsertions, StandardDev of insertion fitness, Standard Error of insertion fitness, and Marking
+        
+        Label 1 and 2: Labels for the column headers for files in the comparison
+        
+        
+        The name of your output file: self-explanatory. Remember to have it end in ".csv".
+        
+        
+    </help>
+    
+</tool>