<tool id="krakentools_combine_kreports" name="Krakentools: Combine multiple Kraken reports" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>into a combined report file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#if $display_headers:
    #for $report in $reports
        ln -s '$report' '${report.element_identifier}' &&
    #end for
#end if

combine_kreports.py 	
    --reports
    #if $display_headers:
        #for $report in $reports
            '${report.element_identifier}'
        #end for
    #else:
        #for $report in $reports
            '${report}'
        #end for
    #end if
    --output '$output'
    $display_headers
    $only_combined
    ]]></command>
    <inputs>
        <param argument="--reports" type="data" multiple="true" format="tabular" label="Kraken report file(s)" />
        <param name="display_headers" type="boolean" checked="true" truevalue="--display-headers" falsevalue="--no-headers" label="display headers in output"/>
        <param name="only_combined" type="boolean" checked="false" truevalue="--only-combined" falsevalue="" label="display only combined read counts and percentages"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
            <param name="display_headers" value="--no-headers"/>
            <output name="output" file="combined_kreport.tabular"/>
        </test>
        <test>
            <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
            <param name="display_headers" value="--no-headers"/>
            <param name="only_combined" value="--only-combined"/>
            <output name="output" file="only_combined_count.tabular"/>
    	</test>
        <test>
            <param name="reports" value="beta_kreport_1.tabular,beta_kreport_3.tabular"/>
            <param name="display_headers" value="--display-headers"/>
            <param name="only_combined" value="--only-combined"/>
	    <output name="output">
		 <assert_contents>
		      <has_text text="#Number of Samples:"/>
		      <has_text text="#S1"/>
		      <has_text text="#S2"/>
		      <has_text text="#perc"/>
		 </assert_contents>
	    </output>
        </test>
    </tests>
    <help><![CDATA[
KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results. This script combines multiple Kraken reports into a combined report file.

Input
------
Kraken-style reports to combine

Output
------
Combine Kraken reports

Input file format (tab-delimited)
   - percentage of total reads
   - number of reads (including reads within subtree)
   - number of reads (only at this level)
   - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
   - NCBI taxonomic ID
   - name of level

Output file format (tab-delimited)
   - percentage of total reads (for summed reads)
   - combined number of reads (including reads within subtree)
   - combined number of reads (only at this level)
   - S1_all_reads, S1_lvl_reads, S2_all_reads, S2_lvl_reads, ...etc.
   - taxonomic classification level (U, D, P, C, O, F, G, S,...etc)
   - NCBI taxonomic ID
   - name of level

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