<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" >

    <description>
      performs QC on BAM files for gene abundances and sample correlation
    </description>

    <requirements>
	<requirement type="package">BAMqc</requirement>
	<requirement type="package">samtools</requirement>
	<requirement type="package">R</requirement>
    </requirements>

    <command interpreter="sh">
    
      BAMqc.sh 

      -r '${refdb}'

      -f '${attrID}'
      
      -R '${rRNAdb}'

      -s '$stranded'

      -o "$output"

      #set $core = len($files)
      
      -p $core

      #if str($cond_adv_options.adv_options) == 'yes':
        -q '$cond_adv_options.mapq'
      #end if

      #for $file in $files
        '$file.input'
        '$file.input.tag'
      #end for

    </command>

    <inputs>    
      <repeat name="files" title="BAM files" min="1">
        <param format="bam" name="input" type="data" label="Files for QC" />
      </repeat>
      
      <param name="refdb" type="select" label="Reference gene model (GTF)">
        <options from_data_table="gene_GTF_database" />
      </param>

      <param name="attrID" type="text" size="50" value="gene_id" label="Feature ID name" help="Summing reads based on gene (gene_id) or transcript (transcript_id.">
        <sanitizer>
	  <valid initial="none">
	    <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." />
	  </valid>
	</sanitizer>
      </param>

      <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)">
        <options from_data_table="rRNA_BED_database" />
      </param>

      <param name="stranded" type="select" label="Strandedness">
        <option value="yes">Yes - Read from stranded library</option>
        <option value="no">No - Reads from unstranded library</option>
        <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option>
     </param>
            
       <conditional name="cond_adv_options">
         <param name="adv_options" type="select" label="Set advanced options">
	   <option value="no" selected="true">No</option>
	   <option value="yes">Yes</option>
	 </param>

	 <when value="yes">
	   <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" />
	 </when>

	 <when value="no" />	
      </conditional>

    </inputs>

    <outputs>
     <data format="html" name="output" label="BAM QC on $on_tag_string" /> 
      <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" />
    </outputs>

    <help>

**What it does**

This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample.

-----

The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_.

ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_.

.. _CSHL: `Cold Spring Harbor Laboratory`_
.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC
.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/
.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/
.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html

    </help>
</tool>