Mercurial > repos > antmarge > compgenes

changeset 6:707a1c043b61 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author antmarge
date Wed, 29 Mar 2017 14:53:57 -0400
parents d8af20d51725
children 9c995a9f974d
files compGenes.xml
diffstat 1 files changed, 53 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compGenes.xml	Wed Mar 29 14:53:57 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>