comparison tools/protein_analysis/signalp3.xml @ 9:e52220a9ddad draft

Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).

8:976a5f2833cd

<tool id="signalp3" name="SignalP 3.0" version="0.0.9">
    <description>Find signal peptides in protein sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">
      signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
      ##Set the number of threads in the runner entry in universe_wsgi.ini
      ##which (on SGE at least) will set the $NSLOTS environment variable.
      ##If the environment variable isn't set, get "", and defaults to one.
    </command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
        <param name="organism" type="select" display="radio" label="Organism">
            <option value="euk">Eukaryote</option>
            <option value="gram+">Gram positive</option>

9:e52220a9ddad

<tool id="signalp3" name="SignalP 3.0" version="0.0.10">
    <description>Find signal peptides in protein sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">
      signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
      ##Set the number of threads in the runner entry in universe_wsgi.ini
      ##which (on SGE at least) will set the $NSLOTS environment variable.
      ##If the environment variable isn't set, get "", and defaults to one.
    </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="organism" type="select" display="radio" label="Organism">
            <option value="euk">Eukaryote</option>
            <option value="gram+">Gram positive</option>