<tool id="vcf_snp" name="vcf to snp" version="0.5">
    <description>vcf to snp for fasta</description>
    <requirements>
       <!-- Should just use the filter snp that's installed in the path -->
           
       </requirements>

## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
## ! We only have a simple single command here.
    <command interpreter="python">
        vcf_snp.py
        -s ${vcf}
        -p ${pos}
        -o output.txt;
        echo ${vcf.name} > name.txt;
        cut -f2 output.txt >seq.txt;
        paste name.txt seq.txt> output2.txt
        
    </command>

    <inputs>
        <param  name="vcf" type="data" label="vcf" help=""/>
        <param  name="pos" type="data" label="positions" help=""/>
        
    </inputs>

    <outputs>
        <data format="tabular" name="output_file" label="${vcf}" from_work_dir="output2.txt">
            </data>
    </outputs>
    
    <tests>
    <!-- Empty -->
    </tests>

    <help>
        
.. class:: infomark

**What it does**

Transforms a vcf into a snp tab file. Has to take the nucleotide from the reference column when identical.

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

.. class:: infomark

**Tool Author**

Brigida Rusconi


    </help>
</tool>