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<tool id="PCA" name="PCA" version="1">
  <description> PCA analysis of VINYL scores is used to identify the presence of possible groups/sub-groups of patients</description>
  <requirements>
    <requirement type="package" >perl</requirement>
    <requirement type="package" >r-base</requirement>
  </requirements>
  <command> <![CDATA[
	ln -s $__tool_directory__/PCA.R 2>$log &&
	ln -s $fileR fileR &&
	ln -s $fileC fileC &&
	

	perl $__tool_directory__/makeToM.pl 
	
	####INPUT
	fileR fileC

	###OUTPUT
	$ofile
 	
	2>>$log



    ]]>
  </command>
  <inputs>
	<param format="vcf" name="fileR" type="data" label="affected" help="vcf file with VINYL scores. Affected individuals "/>
	<param format="vcf" name="fileC" type="data" label="healthy" help="vcf file with VINYL scores. Unaffected individuals"/>
  </inputs>
  <outputs>
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
    <data format="png" name="ofile" label="${tool.name} on ${on_string}: png "/>
  </outputs>
  <stdio>
  </stdio>
  <tests>
      <test>
        <param name="fileR" value="Galaxy28-[Affected_vinyl_scored.vcf].vcf" ftype="vcf" />
        <param name="fileC" value="Galaxy25-[Healthy_vinyl_scored.vcf].vfc" ftype="vcf" />
        <output name="ofile" file="PCA_output_test.png" ftype="png" />
      </test>
  </tests>
  <help>
**What it does**
VINYL is a software designed to assist in variant prioritization in medium-large cohort of patients. The program computes an aggregate score, which is based on an extensive collection of publicly available annotations, in order to identify/prioritize variants that are likely to be pathogenic or have a clinical significance. In order to derive an optimal cut off score for the variants, VINYL uses a strategy based on "survival analysis", where the pathogenicity score distribution of the affected individuals is compared with a matched cohort of unaffected individuals.
To facilitate the usage of the software, VINYL is provided in the form of a public Galaxy instance, based on the Laniakea suite. To ensure the maximum level of security, VINYL uses Encrypted data volumes for the storage of the data.



**Important Usage Note**
This wrapper provides the module of VINYL that performs PCA analysis of score distribution to identify groups/subgroups of patients and/or samples. Two input files need to be provided, both in vcf format. The first file must contain VINYL scores for affected individuals, the second, equivalent score for unaffected controls. Both files can be obtained by running VINYL on annovar-annotated vcf-files (see the manual and the VINYL wrapper for further explanations). 
See the "survival" and the "VINYL" utilities in the for the delineation of the  score cut-off value and the calculation of individual scores from a single vcf file.
A complete workflow that automates the exectuion of VINYL is avaiable at XXX
 
A complete workflow that automates the exectuion of VINYL is avaiable at XXX


  </help>
  <citations>
  </citations>
</tool>