<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0">
  <expand macro="version_command" />
  <expand macro="requirements" />
  <expand macro="stdio" />
  <description>
        view report of classification for multiple samples
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command>
      <![CDATA[

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

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