<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>K-mer counting and filtering of reads</description>
    <xrefs>
        <xref type='bio.tools'>kmc</xref>
    </xrefs> 
    <macros>
	  <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" /> 
    <command><![CDATA[
	    kmc
	    -t\${GALAXY_SLOTS:-4}
	    #if $params.k:
	    	-k'$params.k'		
	    #end if
	    #if $params.m:
	        -m'$params.m'
	    #end if
	    #if $params.j:
	       -j'$statistic'
	    #end if
	    #if $params.exclude_length:
	       -ci'$params.exclude_length'
	    #end if
	    #if $params.max_counter_value:
	       -cs'$params.max_counter_value'
	    #end if
            #if $input_file.is_of_type("fastq"):
               -fq
            #elif $input_file.is_of_type("fasta"):
               -fm
            #elif $input_file.is_of_type("bam"):
               -fbam
            #elif $input_file.is_of_type("kmc_suf"):
               -fkmc
            #end if
	    $input_file
	    db
	    . 

	    ]]></command>
    <inputs>
	    <expand macro="macro_input" />
	    <section name="params" title="parameter" expanded="false">
                    <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" />
		    <param argument="-m" type="integer" value="12" label="max amount of RAM in GB (from 1 to 1024); default: 12" />
		    <param name="signature_length" arguments="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/>
		    <param name="exclude_length" arguments="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
		    <param name="max_counter_value" arguments="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/>
		    <param name="exclude_kmer_occurence" arguments="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
		    <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/>
	    </section>
    </inputs>
    <outputs>
	    <data format="json" name="statistic" label="${tool.name} on ${on_string}">
		   <filter>params['j']</filter>
	    </data>
	  <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
	          <data format="binary" name="db.kmc_suf" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_suf" />
                  <data format="binary" name="db.kmc_pre" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_pre" />
	  </collection>
    </outputs>
	
    <tests>
	 <test>
            <!-- #1 test fastq with common parameters -->
	    <param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/>
            <param name="k" value="25" />
            <param name="m" value="12" />
	    <param name="p" value="9" />
	    <param name="ci" value="2" />
            <param name="cs" value="255" />
	    <output name="db.kmc_suf" file="db.kmc_suf" ftype="binary" />
	    <output name="db.kmc_pre" file="db.kmc_pre" ftype="binary" />
        </test>
        <test>
            <!-- #2 test fasta with common parameters -->
            <param name="input_file" value="contigs.fa" ftype="fasta"/> 
            <param name="k" value="27" />
            <param name="m" value="24" />
            <param name="ci" value="2" />
            <param name="cs" value="255" />
            <param name="fm" value="-fm" />
            <output name="contig_kmer27.kmc_suf" file="contig_kmer27.kmc_suf" ftype="binary" />
            <output name="contig_kmer27.kmc_pre" file="contig_kmer27.kmc_pre" ftype="binary" />
        </test>
   </tests>
    <help><![CDATA[
	    
.. class:: infomark

**What it does**
	    
*K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.*


**Input**
	    
- input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. 

**Example:**

- kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/
- kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/

**Output**

- filename.res.kmc_suf
- filename.res.kmc_pre

 
.. class:: infomark
	    
**References**
	    
More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_.
	]]></help>
     <citations>
        <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation>
	<citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation>
	<citation type="doi">DOI: 10.1186/1471-2105-14-160</citation>
    </citations>
</tool>