annotate data_manager/data_manager_sam_fasta_index_builder.xml @ 8:3ec5c51384e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"

<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.5" profile="19.05">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="1.14">samtools</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/data_manager_sam_fasta_index_builder.py'
        '${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 fasta_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="sam_fasta_data_manager.json"/>"
        </test>
    </tests>

    <help>
.. class:: infomark

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