<?xml version='1.0' encoding='UTF-8'?>
<tool id='snp_sites' name='Finds SNP sites' version='0.1.0'>
   <description>from a multi-FASTA alignment file</description>	
   <requirements>
      <requirement type='package' version='2.3.2'>snp-sites</requirement>
   </requirements>
   <version_command>snp-sites -V</version_command>
   <command detect_errors='aggressive'><![CDATA[
snp-sites 
-mvp 
-o output 
'$input_fasta'
]]></command>
   <inputs>
        <param name='input_fasta' format='fasta' type='data' label='FASTA file' />
   </inputs>
   <outputs>
        <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA' from_work_dir='output.snp_sites.aln'/>
        <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'/>
        <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip' from_work_dir='output.phylip'/>
   </outputs>
   <tests>
      <test>
         <param name='input_fasta' value='input.fasta' ftype='fasta' />
         <output name='output_fasta' value='output.fasta' ftype='fasta' />
         <output name='output_vcf' value='output.vcf' ftype='vcf' />
         <output name='output_phylip' value='output.phylip' ftype='phylip' />
      </test>
   </tests>
   <help>
   <![CDATA[
   
**SNP-sites**

This tool can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.

**Input FASTA format:**

The first sequence will be taken as a reference.

.. code-block::

  >sample1
  AGACACAGTCAC

  >sample1
  AGACAC----AC

  >sample1
  AAACGCATTCAN

**Output files:**

The output of the tool are three different files in following format:

- a multi fasta alignment,
- relaxed phylip format and,
- VCF.

The VCF file for the above specified input is

The output of the tool are three different files in following format:

- a multi fasta alignment,
- relaxed phylip format and,
- VCF.

The VCF file for the above specified input is

=====   === ==  === ===    ====    ======  ====    ======  ======= ======= =======
CHROM   POS ID  REF ALT    QUAL    FILTER  INFO    FORMAT  sample1 sample1 sample1
-----   --- --  --- ---    ----    ------  ----    ------  ------- ------- -------
1       2   .   G   A      .       .       .       GT      0       0       1
-----   --- --  --- ---    ----    ------  ----    ------  ------- ------- -------
1       5   .   A   G      .       .       .       GT      0       0       1
-----   --- --  --- ---    ----    ------  ----    ------  ------- ------- -------
1       8   .   G   .,T    .       .       .       GT      0       1       2
=====   === ==  === ===    ====    ======  ====    ======  ======= ======= =======

Thus the tool identified three variations (SNPs): in 2nd, 5th, and 8th positions (A instead of G, G instead of A, and unknown nucleotide or T instead of G, respectively).


	]]>
    </help>
	<citations>
        <citation type="doi">10.1099/mgen.0.000056</citation>
    </citations>
</tool>