<?xml version="1.0"?>
<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="@WRAPPER_VERSION@">
    <description>view report of classification for multiple samples</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    #set $names = []

    #for $input_count, $input_classification in enumerate( $classification ):
        #set $name_base = str( getattr( $input_classification, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
        #set $name = $name_base
        #set $i = 1
        #while $name in $names:
            #set $name = "%s_%s" % ( $name_base, $i )
            #set $i = $i + 1
        #end while
        #silent $names.append( $name )
        ln -s '${input_classification}' '${name}' &&
    #end for

    @SET_DATABASE_PATH@ &&

    kraken-mpa-report
        @INPUT_DATABASE@
        #for $name in $names:
            '${name}'
        #end for

        ${show_zeros}
        ${header_line}

        > '$output_report'
    ]]></command>
    <inputs>
        <param name="classification" format="tabular" label="Kraken output" multiple="True" type="data" />
        <param name="show_zeros" argument="--show-zeros" type="boolean" falsevalue=""  truevalue="--show-zeros" checked="False"
               label="Display taxa even if they lack a read in any sample" />
        <param name="header_line" argument="--header-line" type="boolean" truevalue="--header-line" falsevalue="" checked="False"
               label="Display a header line indicating sample IDs"/>

        <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" ftype="tabular" file="kraken_mpa_report_test1_output.tab" />
        </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 experiments, conditions, locations, etc.

-----

**Output**

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

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