<tool id="effectiveT3" name="Effective T3" version="0.0.11">
    <description>Find bacterial effectors in protein sequences</description>
    <requirements>
        <requirement type="package" version="1.0.1">effectiveT3</requirement>
    </requirements>
    <version_command interpreter="python">effectiveT3.py --version</version_command>
    <command interpreter="python">
effectiveT3.py $module.fields.path
#if $restrict.type=="cutoff":
  cutoff=$restrict.cutoff
#else:
  $restrict.type
#end if
$fasta_file $tabular_file</command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
        <param name="module" type="select" display="radio" label="Classification module">
            <options from_file="effectiveT3.loc">
                <column name="value" index="0"/>
                <column name="name" index="1"/>
                <column name="path" index="2"/>
            </options>
        </param>
        <conditional name="restrict">
            <param name="type" type="select" label="Cut-off setting">
                <option value="selective">Selective (threshold set in module)</option>
                <option value="sensitive">Sensitive (threshold set in module)</option>
                <option value="cutoff">User defined cut-off</option>
            </param>
            <when value="selective" />
            <when value="sensitive" />
            <when value="cutoff" >
                <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1"  />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="$module.value_label results" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="module" value="animal" />
            <param name="type" value="selective" />
            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
            <param name="module" value="plant" />
            <param name="type" value="sensistive" />
            <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
**What it does**

This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.

The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):

====== ==============================================================================
Column Description
------ ------------------------------------------------------------------------------
     1 Sequence identifier
     2 Sequence description (from the FASTA file)
     3 Score (between 0 and 1, or negative for an error such as a very short peptide)
     4 Predicted effector (true/false)
====== ==============================================================================


**References**

Jehl, Arnold and Rattei.
Effective - a database of predicted secreted bacterial proteins
Nucleic Acids Research, 39(Database issue), D591-5, 2011.
http://dx.doi.org/10.1093/nar/gkq1154

Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
Sequence-based prediction of type III secreted proteins.
PLoS Pathog. 5(4):e1000376, 2009.
http://dx.doi.org/10.1371/journal.ppat.1000376

http://effectors.org/

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
    </help>
</tool>