--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BAM_preprocessingPairs.xml	Mon Jun 11 12:55:48 2012 -0400
@@ -0,0 +1,77 @@
+<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>