comparison data_manager/picard_index_builder.xml @ 3:0663d25e619c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f

2:a8a705f6be94

<tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="0.0.1">
    <description>builder</description>
    <requirements>
        <requirement type="package" version="1.56.0">picard</requirement>
    </requirements>
    <command interpreter="python">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>
    <stdio>
        <exit_code range=":-1" />
        <exit_code range="1:" />
    </stdio>
    <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>

3:0663d25e619c

<tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1">
    <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>

    <help>
.. class:: infomark

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