<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>
		<requirement type="package" version="0.1.18">samtools</requirement>
		<requirement type="package" version="1.3.12">gzip</requirement>
  		<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 
  	-j "\$JAVA_JAR_PATH/MergeSamFiles.jar"
  </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>