view vcf_to_snp.xml @ 1:032d2c8cf8ae draft

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<tool id="vcf_snp" name="vcf to snp" version="0.1">
    <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}
        -o output.txt;
        cut -f1 output.txt > header.txt | cut -f2- output.txt > seq.txt;
        cat seq.txt | sed 's/[[:blank:]]//g' >seq2.txt;
        paste header.txt seq2.txt >tab.txt;
       
        
    </command>

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

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

    <help>
        
.. class:: infomark

**What it does**

Transforms a vcf into a snp tab file

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

.. class:: infomark

**Tool Author**

Brigida Rusconi


    </help>
</tool>