<tool id="effectiveT3" name="Effective T3" version="0.0.20">
    <description>Find bacterial effectors in protein sequences</description>
    <requirements>
        <requirement type="package" version="1.0.1">effectiveT3</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/effectiveT3.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/effectiveT3.py '$module.fields.path'
#if $restrict.type=="cutoff":
  'cutoff=$restrict.cutoff'
#else:
  '$restrict.type'
#end if
'$fasta_file' '$tabular_file'
    </command>
    <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="Effective T3 $module.value_label on ${on_string}" />
    </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" lines_diff="2"/>
        </test>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="module" value="std_2_0_2" />
            <param name="type" value="cutoff" />
            <param name="cutoff" value="0.8" />
            <output name="tabular_file" file="four_human_proteins.effectiveT3_std2.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
            <param name="module" value="plant" />
            <param name="type" value="sensitive" />
            <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**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
https://doi.org/10.7717/peerj.167

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

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

See also 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>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/nar/gkq1154</citation>
        <citation type="doi">10.1371/journal.ppat.1000376</citation>
    </citations>
</tool>