view data_manager/data_manager_gatk_picard_index_builder.xml @ 1:f6052387284e

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<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement>
    </requirements>
    <command interpreter="python">
        data_manager_gatk_picard_index_builder.py "${out_file}" \
            --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \
            --fasta_filename "${all_fasta_source.fields.path}" \
            --fasta_dbkey "${all_fasta_source.fields.dbkey}" \
            --fasta_description "${all_fasta_source.fields.name}" \
            --data_table_name "gatk_picard_indexes"
    </command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param type="text" name="sequence_name" value="" label="Name of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>

    <help>

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically. 

    </help>
</tool>