view data_manager/data_manager_select_index_by_path.xml @ 32:f33444a00082 draft

planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit fe7f241c6a14c4a836368a8a555b91555c26d642

<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.3">
    <requirements>
        <!-- Away with python 2! -->
        <requirement type="package" version="3.5">python</requirement>
        <requirement type="package" version="3.12">pyyaml</requirement>
    </requirements>
    <description>Link to indexes on the filesystem that have already been built</description>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/path_name_value_key_manager.py
        --value "${value}"
        --dbkey "${dbkey}"
        --name "${name}"
        --path "${path}"
        --data_table_name "${data_table_set.data_table}"
        --json_output_file "${json_output_file}"
        #if $data_table_set.data_table == "rnastar_index2"
        --extra-columns '{"with-gtf": "$data_table_set.with_gtf"}'
        #end if
        ]]></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" />
        <conditional name="data_table_set">
            <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>
                <option value="rnastar_index2">rnastar_index2</option>
            </param>
            <when value="rnastar_index2">
                <param name="with_gtf" type="select" value="" label="Index with embedded gtf?">
                    <option value="0">No</option>
                    <option value="1">Yes</option>
                </param>
            </when>
        </conditional>
    </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>