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<?xml version="1.0"?>
<tool id="Genetic_Marker_Design_2" name="Design primers to features">
  <description>Design PCR Primers to Features</description>
 <command interpreter="python -W ignore">
      #if 'Yes' in $uMelt.value
          design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u >  $primer_outputfile
      #else
          design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size  >  $primer_outputfile  
      #end if
       </command>

  <inputs>
    <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
    <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
    <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param>
<param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
     <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
 <param name="uMelt"  type="select"  label="uMelt prediction for HRM">
            <option value="No" selected= "true">No</option>
            <option value="Yes">Yes</option>
         </param>
 </inputs>
  <outputs>
     <data format="tabular"  name="primer_outputfile" />
  </outputs>
  <stdio>
        <exit_code range="1:" level="fatal" description="Fatal Error" />
  </stdio>
<help>
.. class:: infomark

**TIP**

This tool designs primer pairs to flank features
Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah

It takes 

* an input reference sequence file
* a gff3 file containing feature information
* a single column file containing list of features  

----

**Example**

--input GFF

::

 PGSC0003DMB000000001    samtools        SNP     6345    6346    4.84    .       .       ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6345;Variant_seq=C;Reference_seq=T;Total_reads=2
 PGSC0003DMB000000001    samtools        SNP     6453    6454    18      .       .       ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6453;Variant_seq=T;Reference_seq=G;Total_reads=8
 PGSC0003DMB000000001    samtools        SNP     7255    7256    149     .       .       ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7255;Variant_seq=G;Reference_seq=T;Total_reads=14
 PGSC0003DMB000000001    samtools        SNP     7371    7372    86.8    .       .       ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7371;Variant_seq=C;Reference_seq=T;Total_reads=9
 PGSC0003DMB000000001    samtools        SNP     8288    8289    10.7    .       .       ID=PGSC0003DMB000000001:SAMTOOLS:SNP:8288;Variant_seq=A;Reference_seq=G;Total_reads=5


--input features

::

	PGSC0003DMB000000001:SAMTOOLS:SNP:1012901
	PGSC0003DMB000000001:SAMTOOLS:SNP:1021771
	PGSC0003DMB000000001:SAMTOOLS:SNP:1025761
	PGSC0003DMB000000001:SAMTOOLS:SNP:1026717
	PGSC0003DMB000000001:SAMTOOLS:SNP:1026834
	PGSC0003DMB000000001:SAMTOOLS:SNP:1029542


--output columnar data

::

 PGSC0003DMB000000001:SAMTOOLS:SNP:1012901 AGAGGTCGGCTCTCTAGTAGCA GGGGATCCACTAACTATGTCACTT 86
 PGSC0003DMB000000001:SAMTOOLS:SNP:1021771 CCTATGCGAGAAAGGGACAC GCCCTTCCATGTTGTACGAG 100
 PGSC0003DMB000000001:SAMTOOLS:SNP:1025761 TGTGAGTAACTTAGTGTCCTACGTCAA CACTCAATGAGCCAAAGCAA 92
 PGSC0003DMB000000001:SAMTOOLS:SNP:1026717 TTCCTAAGTCATGGGAAAGCA AGTTCATCCAAGGCAAGCAT 76
 PGSC0003DMB000000001:SAMTOOLS:SNP:1026834 AATGAAGTGACTGGGGAGGA TGCTGGTCGAAGCTTTCTTT 98
 PGSC0003DMB000000001:SAMTOOLS:SNP:1029542 TAACCAGAAAGTCCGGATGG TTCTGAAGTCAAGTGGGGAGA 75

-----------------------

*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum

</help>

</tool>