comparison tools/protein_analysis/psortb.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="Psortb" name="psortb" version="0.0.7">
    <description>Determines sub-cellular localisation of bacterial/archaeal 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>
    <requirements>
        <requirement type="binary">psort</requirement>
        <requirement type="package">psort</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">psortb.py --version</version_command>
    <command interpreter="python">
psortb.py "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
##If the environment variable isn't set, get "", and python wrapper
##defaults to four threads.
    </command>
    <inputs>
        <param format="fasta" name="sequence" type="data"
               label="Input sequences for which to predict localisation (protein FASTA format)" />
        <param name="type" type="select"

20:a19b3ded8f33

<tool id="Psortb" name="psortb" version="0.0.9">
    <description>Determines sub-cellular localisation of bacterial/archaeal 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>
    <requirements>
        <requirement type="package">psort</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/psortb.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/psortb.py "\$GALAXY_SLOTS" '$type' '$long' '$cutoff' '$divergent' '$sequence' '$outfile'
    </command>
    <inputs>
        <param format="fasta" name="sequence" type="data"
               label="Input sequences for which to predict localisation (protein FASTA format)" />
        <param name="type" type="select"