<tool id="svdetect_preprocessing" name="BAM preprocessing">

  <description>to get abnormal pairs</description>

  <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name
	#if $newBam.pairNormal=="yes" 
	-d -x '$normBAM'
	#end if
	'$inputBam'
  </command>

  <inputs>
    <param name="sample_name" type="text" value="sample" label="Sample Name"/>
    <param name="inputBam" type="data" format="bam" label="BAM input file"/>
    <param name="readType" type="select" label="Read type">
	<option value="1">Illumina</option>
	<option value="0">SOLiD</option>
   </param>
   <param name="pairType" type="select" label="Library type">
	<option value="1">Paired-end</option>
	<option value="0">Mate-Pair</option>
   </param>
   <conditional name="newBam">
   <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam">
	<option value="no">No</option>
	<option value="yes">Yes</option>
   </param>
    <when value="yes">
	  <!-- do nothing here -->
    </when>
    <when value="no">
	 <!-- do nothing here -->
    </when>
   </conditional>
   <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/>
   <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/>
   <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/>
   <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/>
  </inputs>

  <outputs>
    <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/> 
    <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/>
    <data format="bam" name="normBAM" label="${$sample_name}.norm.bam">
    <filter>newBam['pairNormal'] == 'yes'</filter>
    </data> 
  </outputs>

  <help>

**What it does**

Bam_preprocessingPairs - Version 0.4b

Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect.

From all pairs mapped onto the reference genome, this script outputs abnormal pairs:

	* mapped on two different chromosomes
	* with an incorrect strand orientation and/or pair order
	* with an insert size distance +- sigma threshold

into a file prefix.ab.bam/sam sorted by read names
    
-BAM/SAM File input format only.
  
SAMtools required for BAM files

-----

.. class:: infomark

Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.

  </help>

</tool>