comparison data_manager/data_manager_snpEff_download.xml @ 3:e5a471c4630e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f

2:984733fcab49

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.1">snpEff</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">
        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
          --genome_version "$genome_version" "$out_file"
        </command>
    <inputs>
        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
            <help>https://snpeff-data.galaxyproject.org/databases/</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>

Please cite:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

    </help>
      <citations>
        <citation type="doi">10.4161/fly.19695</citation>
      </citations>
</tool>

3:e5a471c4630e

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
    <description>Download a new database</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPEFF_JAR_PATH@ &&
        python $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
          --genome_version "$genome_version" "$out_file"
        ]]>
    </command>
    <inputs>
        <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
            <help>https://snpeff-data.galaxyproject.org/databases/</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>

Please cite:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]

    </help>
    <expand macro="citations" />
</tool>