comparison tools/protein_analysis/promoter2.xml @ 18:eb6ac44d4b8e draft

Suite v0.2.8, record Promoter 2 verion + misc internal updates

17:e6cc27d182a8

<tool id="promoter2" name="Promoter 2.0" version="0.0.8">
    <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 "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
        ##If the environment variable isn't set, get "", and the python wrapper
        ##defaults to four threads.
    </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}" />
    </outputs>
    <requirements>
        <requirement type="binary">promoter</requirement>
    </requirements>
    <tests>
        <test>
            <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
            <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
        </test>

18:eb6ac44d4b8e

<tool id="promoter2" name="Promoter 2.0" version="0.0.10">
    <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>
    <requirements>
        <requirement type="binary">promoter</requirement>
        <requirement type="package">promoter</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">promoter2.py --version</version_command>
    <command interpreter="python">
        promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
        ##If the environment variable isn't set, get "", and the python wrapper
        ##defaults to four threads.
    </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}" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
            <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
        </test>