view data_manager/data_manager_select_index_by_path.xml @ 5:1abe9fb7c454 draft

planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9a42a858c5039edd1062e7a8a315c91c2c213000

<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="text" value="" label="data table for the index">
          <option value='all_fasta'>all_fasta --no_prefix</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='gemini_databases'>gemini_databases</option>
          <option value='gene_transfer'>gene_transfer</option>
          <option value='hisat2_indexes'>hisat2_indexes</option>
          <option value='kallisto_indexes'>kallisto_indexes --no-prefix</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>