<tool id="compStrains" name="Compare Strains" version="0.1.0">
    
    <!-- Margaret Antonio  17.01.08 -->

    <description> compare gene aggregate fitness from two different experiments for two different strains (genomes)</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</requirement>
        <requirement type="package" version="2.121">perl_data_dumper</requirement>
        <requirement type="package" version="2.12">perl_file_path</requirement>
        <requirement type="package" version="5.24.1">perl_file_basename</requirement>
    </requirements>
    
    <command interpreter="perl">
        compStrains.pl
        -input1 $input1
        -input2 $input2
        -c $cfile
        -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"/>
        <param name="cfile" type="data" label="Conversion file for homologous genes"/>


    </inputs>
   
    <outputs>
        <data format="csv" name="outfile"  />
    </outputs>
    
    <help>
        **What it does**
        
        This tool compares genes for different strains under a single condition. It takes two geneAgregate outputs and compares them calculating the difference in mean fitness for each gene. A tab-delimited conversion file, with one set of gene homologs per line is required Example usage: compare two strains of  in presence of an antibiotic. For the same strain/genome, where gene ids are the same, use compGenes.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
        
        Conversion File: Tab-delimited file of homologous genes for the two strains. One set of homologs per line, with each gene id separated by a tab.
        
        
        
    </help>
    
</tool>