<tool id="kraken-translate" name="Kraken-translate" version="1.0.0">
    <description>
        convert taxonomy IDs to names
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>
        <![CDATA[
        @SET_DATABASE_PATH@ &&
        kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}"
        ]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken classification" name="input" type="data" />
        <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" />
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
    </outputs>
    <help>
        <![CDATA[
**What it does**

The file sequences.labels generated by the above example is a text file with two tab-delimited columns, and one line for each classified sequence in sequences.fa; unclassified sequences are not reported by kraken-translate. The first column of kraken-translate's output are the sequence IDs of the classified sequences, and the second column contains the taxonomy of the sequence. For example, an output line from kraken of:

C     SEQ1    562     36      562:6

Would result in a corresponding output line from kraken-translate of:

SEQ1  root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli

Alternatively, kraken-translate accepts the option --mpa-format which will report only levels of the taxonomy with standard rank assignments (superkingdom, kingdom, phylum, class, order, family, genus, species), and uses pipes to delimit the various levels of the taxonomy. For example, kraken-translate --mpa-format --db $DBNAME with the above example output from kraken would result in the following line of output:

SEQ1  d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli

Taxonomy assignments above the superkingdom (d__) rank are represented as just "root" when using the --mpa-report option with kraken-translate.
        ]]>
    </help>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <expand macro="citations" />
</tool>