<tool id="tradis_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@TOOL_VERSION@+galaxy@VERSION@">
    <description></description>
    <macros>
          <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
        <![CDATA[
            tradis_gene_insert_sites -trim3 '$trim3' -trim5 '$trim5' '$input_annot' '$input_counts'  
        ]]>
    </command>
    
    <inputs>
        <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
        <param name="input_annot" type="data" format="embl" label="EMBL file containing the reference genome annotations"/>
       <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
       
    </inputs>
    
    <outputs>
        <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv" label="${tool.name} on ${on_string}"/>
    </outputs>
    
    <tests>
        <test>
            <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
            <param name="input_annot" ftype="embl" value="tiny_ref.embl"/>
            <param name="trim3" ftype="float" value="0"/>
            <param name="trim5" ftype="float" value="0"/>
            <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.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_gene_insert_sites that combine the counts at each position and an annotation file to provide the number of reads and insertion for each feature.

-----

**Output files**

The tool outputs a table containing the columns :
-   locus_tag
-   gene_name
-   ncrna : Is the feature a non-coding DNA. 1=yes, 0=no.
-   start
-   end
-   strand
-   read_count : Numer 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>