annotate data_manager/data_manager_gatk_picard_index_builder.xml @ 7:0f85d523291e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder commit a54e50916ebdb0858b049cdc549a43df801e1a71

<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.2" profile="23.0">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="0.1.18">samtools</requirement>
        <requirement type="package" version="1.56.0">picard</requirement>
        <requirement type="package" version="3.8.3">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
        python '$__tool_directory__/data_manager_gatk_picard_index_builder.py' '${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 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>

    <help>
.. class:: infomark

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