comparison tools/protein_analysis/rxlr_motifs.xml @ 20:a19b3ded8f33 draft

v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes

19:f3ecd80850e2

<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.11">
    <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
    <requirements>
        <!-- Need SignalP for all the models -->
        <requirement type="binary">signalp</requirement>
        <requirement type="package">signalp</requirement>
        <!-- Need HMMER for Whisson et al. (2007) -->
        <requirement type="binary">hmmsearch</requirement>
        <requirement type="package">hmmsearch</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">rxlr_motifs.py -v</version_command>
    <command interpreter="python">
      rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
    </command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" /> 
        <param name="model" type="select" label="Which RXLR model?">
            <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
            <option value="Win2007">Win et al. (2007) RXLR</option>
            <option value="Whisson2007" selected="True">Whisson et al. (2007) RXLR-EER with HMM</option>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="$model.value_label" />
    </outputs>

            <param name="model" value="Whisson2007"/>
            <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
    
**Background**

Many effector proteins from oomycete plant pathogens for manipulating the host
have been found to contain a signal peptide followed by a conserved RXLR motif
(Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There

20:a19b3ded8f33

<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.14">
    <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
    <requirements>
        <!-- Need SignalP for all the models -->
        <requirement type="package">signalp</requirement>
        <!-- Need HMMER for Whisson et al. (2007) -->
        <requirement type="package">hmmer2</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/rxlr_motifs.py -v
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/rxlr_motifs.py '$fasta_file' "\$GALAXY_SLOTS" '$model' '$tabular_file'
    </command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" />
        <param name="model" type="select" label="Which RXLR model?">
            <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
            <option value="Win2007">Win et al. (2007) RXLR</option>
            <option value="Whisson2007" selected="true">Whisson et al. (2007) RXLR-EER with HMM</option>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="$model.value_label" />
    </outputs>

            <param name="model" value="Whisson2007"/>
            <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>

**Background**

Many effector proteins from oomycete plant pathogens for manipulating the host
have been found to contain a signal peptide followed by a conserved RXLR motif
(Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There