comparison tools/protein_analysis/effectiveT3.xml @ 2:5a8e09f115f8 draft

Uploaded v0.0.10, adds unit tests. Includes v0.0.9 which checked error codes.

1:e607c342312f

<tool id="effectiveT3" name="Effective T3" version="0.0.8">
    <description>Find bacterial effectors in protein sequences</description>
    <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>
    <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"/>

        </conditional>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="$module.value_label results" />
    </outputs>
    <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):

 * Sequence identifier
 * Sequence description (from the FASTA file)
 * Score (between 0 and 1, or negative for an error such as a very short peptide)
 * Predicted effector (true/false)

**References**

Jehl, Arnold and Rattei.
Effective - a database of predicted secreted bacterial proteins

2:5a8e09f115f8

<tool id="effectiveT3" name="Effective T3" version="0.0.10">
    <description>Find bacterial effectors in protein sequences</description>
    <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"/>

        </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