comparison data_manager/data_manager_snpEff_databases.xml @ 4:a9cace1ee2b7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty

3:821c34cdacb6

<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
	<description>Read the list of available snpEff databases</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_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
        </command>
	<inputs>
	</inputs>
	<outputs>
           <data name="out_file" format="data_manager_json"/>
	</outputs>
        <tests>
            <test>
                <output name="out_file">
                    <assert_contents>
                        <!-- Check that a genome was added -->
                        <has_text text="GRCh38.76" />
                    </assert_contents>
                </output>
            </test>
        </tests>
	<help>

This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
It should only need to be run once for a snpEff version, 
since it populates the SnpEff Download data manager from the snpEff config file.

For information about snpEff:    http://snpEff.sourceforge.net

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>

4:a9cace1ee2b7

<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3k" tool_type="manage_data">
    <description>Read the list of available SnpEff databases</description>
    <requirements>
        <requirement type="package" version="4.3k">snpeff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
    ]]></command>
    <inputs>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh38.76" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool updates the list of SnpEff databases for the SnpEff Download data manager.
It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file.

For information about SnpEff: http://snpeff.sourceforge.net
    ]]></help>
    <citations>
        <citation type="doi">10.4161/fly.19695</citation>
    </citations>
</tool>