<tool id="tradis_essentiality" name="Bio-TraDis Essentiality Predictions" version="@VERSION@">
    <description></description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        <![CDATA[
            ln -s '$input_insert_file' input.csv &&
            tradis_essentiality.R input.csv 
        ]]>
    </command>
    
    <inputs>
        <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/>
    </inputs>
    
    <outputs>

        <data name="ess_genes" format="csv" label="${tool.name} on ${on_string} : Essential genes" from_work_dir="input.csv.essen.csv"/>
        <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string} : Unclassified genes" from_work_dir="input.csv.ambig.csv"/>
        <data name="all_genes" format="csv" label="${tool.name} on ${on_string} : All genes" from_work_dir="input.csv.all.csv"/>
        <data name="qc_results" format="pdf" label="${tool.name} on ${on_string} : QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/>
    </outputs>
    
    <tests>
        <test>
            <param name="input_insert_file" ftype="csv" value="test.csv"/>
            <output name="ess_genes" file="test.csv.essen.csv" compare="sim_size" delta="200" />
            <output name="ambig_genes" file="test.csv.ambig.csv" compare="sim_size" delta="200" />
            <output name="all_genes" file="test.csv.all.csv" compare="sim_size" delta="200" />
        </test>
    </tests>
    <help>
<![CDATA[

**What is does**

Bio-TraDis provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.

tradis_essentiality tool performs an Essentiality analysis using the annotation counts output of tradis_gene_insert_sites tool

-----

**Output files**

-    Essential genes table : Table containing the essential genes
-    Unclassified genes : Table containing genes that couldn't be classified as essential or non essential
-    All genes : Table containing all genes 
-    QC report : PDF file containing the regression plot

All tables contain the following columns:
-   locus_tag
-   gene_name
-   ncrna : Non-coding RNA, 1 if the feature is a non coding DNA, 0 if not.
-   start
-   end
-   strand
-   read_count : Total number of reads mapping on the feature
-   ins_index : Insertion index, number of insertion divided by the gene length
-   gene_length
-   ins_count : Number of insertion within the feature.
-   fcn : Function 
 
-----

**More information**

.. class:: infomark

Additional information about Bio-TraDis can be found at https://github.com/sanger-pathogens/Bio-Tradis
]]>
    </help>

<expand macro="citations" />

 </tool>