comparison tools/protein_analysis/promoter2.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="promoter2" name="Promoter 2.0" version="0.0.2">
    <description>Find eukaryotic PolII promoters in DNA sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">
        promoter2.py "\$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 DNA sequences"/> 
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />

9:e52220a9ddad

<tool id="promoter2" name="Promoter 2.0" version="0.0.3">
    <description>Find eukaryotic PolII promoters in DNA sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">
        promoter2.py "\$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 DNA sequences"/> 
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />