<?xml version="1.0"?>
<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.2.0">
    <description>view report of classification for multiple samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[

#for $input_count, $input_classification in enumerate( $classification ):
    ln -s "${input_classification}" "sample_${input_count}" &&
#end for

@SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@

#for $input_count, $input_classification in enumerate( $classification ):
    "sample_${input_count}"
#end for

${show_zeros}
${header_line}

> "$output_report"
]]>
    </command>
    <inputs>
        <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
        <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" />
        <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" />
        <expand macro="input_database" />
    </inputs>
    <outputs>
        <data format="tabular" name="output_report" />
    </outputs>
    <tests>
        <test>
            <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/>
            <param name="show_zeros" value="--show-zeros"/>
            <param name="header_line" value="--header-line"/>
            <param name="kraken_database" value="test_db"/>
            <output name="output_report" file="kraken_mpa_report_test1_output.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: warningmark

**Note**: the database used must be the same as the one used in the original Kraken run

-----

**What is Does**

Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters::

--show-zeros    Display taxa even if they lack a read in any sample
--header-line   Display a header line indicating sample IDs
                (sample IDs are the filenames)

-----

**Output**

The output of kraken-mpa-report is tab-delimited, with one line per taxon.

]]>
    </help>
    <expand macro="citations" />
</tool>