<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1">
    <description>index builder</description>
    <requirements>
        <requirement type="package" version="0.11.2">salmon</requirement>
    </requirements>
   <macros>
       <token name="@IDX_VERSION@">q5</token>
   </macros>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
            --fasta_filename '${all_fasta_source.fields.path}'
            --fasta_dbkey '${all_fasta_source.fields.dbkey}'
            --fasta_description '${all_fasta_source.fields.name}'
            --kmer_size "${kmer_size}"
            --data_table_name salmon_indexes_versioned
            --index_version @IDX_VERSION@
        ]]>
    </command>
    <inputs>
        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
            <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="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be.  We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>



    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
<![CDATA[
.. class:: infomark

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