annotate data_manager/bowtie2_index_builder.xml @ 5:115f3e61b012 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 47a185ef4aba48923d64570f94a3a7a52d6b41e6"

<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@" profile="18.09">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <macros>
        <token name="@WRAPPER_VERSION@">2.3.5.1</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/bowtie2_index_builder.py'
        '${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 bowtie2_indexes ${tophat2}
    ]]></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" />
        <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
    </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="bowtie2_data_manager.json"/>
        </test>
    </tests>

    <help>
.. class:: infomark

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