view data_manager/picard_index_builder.xml @ 3:ae080ff506fd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"

<tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1+galaxy1" profile="18.09">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="2.7.1">picard</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/picard_index_builder.py'
        '${out_file}'
        --fasta_filename '${all_fasta_source.fields.path}'
        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
        --fasta_description '${all_fasta_source.fields.name}'
        --data_table_name picard_indexes
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence" />
        <param name="sequence_id" type="text" value="" label="ID for sequence" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <output name="out_file" value="picard_index_builder_data_manager.json"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>