<tool id="qualimap_bamqc" name="Analyse SAM/BAM with bamqc" version="1.0.1">
    <!-- Additional info: wrapper compatible with versions ..... -->
    <description>
		to asses mapping quality metrics.
    </description>
    
    <version_command>
		qualimap --version
	</version_command>
    
    <requirements>
        <requirement type="package">qualimap</requirement>
    </requirements>
    
    <command interpreter="perl">
        ## it is recommended that you write a wrapper for your tool
        ## and pass all parameters to that tool, which parses them.
        bamqc_wrapper.pl $configfile
    </command> 
   
    <inputs>
	<param format="sam,bam" name="bam" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
	<param type="boolean" name="c" checked="TRUE" truevalue="-c" falsevalue="" label="paint chromosome limits inside charts" />
	<conditional name="customgtf">
            <param name="upload" type="select" label="BETA! Analyze the alignment data for the regions of interest you provide">
              <option value="yes">Yes</option>
              <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
	      <param name="gff" type="data" format="bed,gtf,gff3" label="Choose your feature annotation file" help="Provide your BED, GTF or GFF file"/>
	      <param name="os" type="boolean" checked="FALSE" truevalue="-os" falsevalue="" label="compute also regions outside stats" help="If checked, the information about the reads that are mapped outside of the regions of interest will be also computed and shown in a separate section" />
	      <param type="select" name="p" label="The sequencing protocol strand specificity" help="Can be non-strand-specific, forward-stranded orreverse-stranded. This information is required to calculate the number of correct strand reads.">
                  <option value="NON-STRAND-SPECIFIC">Non-strand-specific</option>                                        
                  <option value="STRAND-SPECIFIC-FORWARD">Strand-specific forward</option>                                        
                  <option value="STRAND-SPECIFIC-REVERSE">Strand-specific reverse</option>                                        
	      </param>
	    </when>
	    <when value="no"/>
        </conditional>
	<param name="hm" type="text" size="3" value="3" label="minimum size for a homopolymer to be considered in indel analysis" help="Only homopolymers of this size or larger will be considered when estimating homopolymer indels count"/>
	<param name="nr" type="text" size="6" value="1000" label="number of reads in the chunk" help="In order to reduce the load of I/O, reads are analyzed in chunks. Each chunk contains the selected number of reads which will be loaded into memory and analyzed by a single thread. Smaller numbers may result in lower performance, but also the memory consumption will be reduced. The default value is 1000 reads"/>
    </inputs>

    <outputs>
        <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}">
        <!-- <data format="html" name="bamqc_result" label="${tool.name} on ${on_string}" from_work_dir="bamqc_output/qualimapReport.html"> -->
        </data>
    </outputs>

    <configfiles>
      <!-- this config file collects all parameter settings -->
      <configfile name="configfile">
	## first we pass some galaxy environment variables
	galtemp==${__new_file_path__}

	bamqc_result==$bamqc_result
	outputdir==$bamqc_result.files_path
	bam==$bam
	c==$c
	hm==$hm
	nr==$nr
	#if $customgtf.upload=="yes"
	 gff==$customgtf.gff
	 os==$customgtf.os
	 p==$customgtf.p
	#end if
      </configfile>
    </configfiles> 

    <tests>
    </tests>

    <help>
**Tool Overview**

Bamqc_ allows for simply but throroughly checking of the quality of mapping. 

.. _Bamqc: http://qualimap.bioinfo.cipf.es//
        
------

    </help>
</tool>