annotate data_manager/data_manager_select_index_by_path.xml @ 0:5f8d9309058b draft

planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a

<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2">
    <description>path inputer</description>
    <command interpreter="python">
        path_name_value_key_manager.py
        --value "${value}"
        --dbkey "${dbkey}"
        --name "${name}"
        --path "${path}"
        --data_table_name "${data_table}"
        --json_output_file "${json_output_file}"
    </command>
    <inputs>
        <param name="value" type="text" value="" label="value field for the entry.  Defaults to name if left blank." />
        <param name="dbkey" type="text" value="" label="dbkey field for the entry.  Defaults to value if left blank." />
        <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." />
        <param name="path" type="text" value="" label="path field for the entry" />
        <param name="data_table" type="select" value="" label="data table for the index">
          <option value='all_fasta'>all_fasta</option>
          <option value='bowtie2_indexes'>bowtie2_indexes</option>
          <option value='bowtie_indexes'>bowtie_indexes</option>
          <option value='bowtie_indexes_color'>bowtie_indexes_color</option>
          <option value='bwa_mem_indexes'>bwa_mem_indexes</option>
          <option value='bwameth_indexes'>bwameth_indexes</option>
          <option value='fasta_indexes'>fasta_indexes</option>
          <option value='gatk_picard_indexes'>gatk_picard_indexes</option>
          <option value='gene_transfer'>gene_transfer</option>
          <option value='hisat2_indexes'>hisat2_indexes</option>
          <option value='kallisto_indexes'>kallisto_indexes</option>
          <option value='picard_indexes'>picard_indexes</option>
          <option value='tophat2_indexes'>tophat2_indexes</option>
        </param>
    </inputs>
    <outputs>
        <data name="json_output_file" format="data_manager_json"/>
    </outputs>

    <help>
Adds a server path to the selected data table.

The tool will check the path exists but NOT check that it holds the expected data type.

If name is not provided the filename from path less the extension is used.

If value is not provided, the name will be used (or its default)

If dbkey is not provided, the value will be used (or its default)

    </help>
    <citations>
    </citations>

</tool>