--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignCustomAmplicon/alignCustomAmplicon_wrapper.xml	Wed Jan 09 00:24:09 2013 -0500
@@ -0,0 +1,82 @@
+<tool id="alignCustomAmplicon" name="Align Custom Amplicon" version="0.0.1">
+  <description>align amplicon to reference with primers</description>
+  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
+  <requirements><requirement type="package" version="0.1.18">samtools</requirement></requirements>
+  <requirements><requirement type="package" version="1.3.12">gzip</requirement></requirements>
+  <requirements><requirement type="perl-module" version="0.42">Inline-CPP</requirement></requirements>
+  <command interpreter="perl">
+  	alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers 
+  </command>
+
+  <inputs>
+  	<param name="refFile" type="select" label="Select a reference genome">
+		<options from_data_table="all_fasta">
+			<filter type="sort_by" column="2" />
+			<validator type="no_options" message="No indexes are available" />
+		</options>
+	</param>
+  	<param name="read1" type="data" format="fastqsanger,fastqillumina, fastq" label="FASTQ read 1 " help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
+  	<param name="read2" type="data" format="fastqsanger,fastqillumina, fastq" label="FASTQ read 2" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />	
+  	<param name="primers" type="data" format="tabular" label="Primers" help="Primers location and length"/>
+  </inputs>
+  
+  <outputs>
+    <data type="data" format="bam" name="output"/>
+  </outputs>
+  	
+  <help> 
+
+.. class:: infomark
+
+**What it does**
+
+It is an amplicon aligner that uses primers for higher accuracy.
+
+Reads with primers are aligned to the reference, then primers are discarded.
+
+If both reads are long enough, they are aligned with the reference and a consensus alignment is generated.
+
+Otherwise, each read is aligned separately.
+
+Sequences with bad quality reads are discarded. 
+
+
+
+**Input**
+
+ref:
+
+	Fasta file of ref gnome
+
+read1:
+
+	Fastq file of left to right read
+	(Can also be compressed [fastq.gz])
+
+read2:
+
+	Fastq file of right to left read
+	(Can also be compressed [fastq.gz])
+
+primers:
+
+	Text file with primers name and length (see example)
+
+Example primers format::
+
+	#Name_of_amplicon 	length_left 	length_right
+	1:115256345-115256520	23		23
+	1:115256436-115256606	25		22
+	1:115256530-115256724	23		23
+	1:115256532-115256723	23		23
+	4:55151914-55152086	21		23
+	4:55151935-55152132	20		23
+	4:55151991-55152182	23		24
+	4:55591944-55592136	23		24
+	4:55592065-55592263	20		23
+	4:55593504-55593674	24		25
+	...
+
+
+  </help>
+</tool>