<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="1.3.0" profile="19.01">
    <description>index builder</description>
    <requirements>
        <requirement type="package" version="1.3.0">salmon</requirement>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
   <macros>
       <token name="@IDX_VERSION@">q7</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>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="sequence_name"/>
            <param name="sequence_id" value="sequence_id"/>
            <output name="out_file">
                <assert_contents>
                    <has_line line='{"data_tables": {"salmon_indexes_versioned": [{"dbkey": "phiX174", "name": "sequence_name", "path": "sequence_id", "value": "sequence_id", "version": "q7"}]}}' />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
]]>
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
    </citations>
</tool>