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<tool id="survival" name="survival" version="1">
  <description> Survival Analysis. This module of VINYL identifies the optimal score cut-off for the idenfication of likely pathogenic variants </description>
  <requirements>
    <requirement type="package" >r-base</requirement>
  </requirements>
  <command> <![CDATA[
       ### call the .sh to untar the package 
	Rscript --vanilla $__tool_directory__/survival_M.R $csv1 $csv2 $tabular

##Questo è uno script di R, che andrebbe fatto girare dopo che il coso ha
##finito.
##
##Ha in input 3 parametri: 2 sono file che si deve leggere, 1 è il nome
##del file di output (che è un semplice file tabulare)
##
##trovi il tutto a questo link: http://159.149.160.53/coso/survival/
##Inclusi 2 file di esempio
##
##Il comando per farlo girare è
##
##Rscript --vanilla survival.R ALL_DCM.csv test_DCM.csv ofile

    ]]>
  </command>
  <inputs>
    <param format="tabular,csv" name="csv1" type="data" label="affected" help="VINYL Tabular output format file. Affected individuals "/>
    <param format="tabular,csv" name="csv2" type="data" label="healthy" help="VINYL Tabular output format file. Unaffected individuals"/>
  </inputs>
  <outputs>
    <data format="tabular" name="tabular" label="${tool.name} on ${on_string}: tabular output " help="Table with results of the survival analysis."/>
  </outputs>
  <stdio>
     <regex match="error"
            source="stdout"
            level="fatal"
            description="Unknown error encountered" />
  </stdio>
  <tests>
    <test>
      <param format="tabular,csv" name="csv1" value="VINYL_input1.tabular" ftype="tabular" />
      <param format="tabular,csv" name="csv2" value="VINYL_input2.tabular" ftype="tabular" />
      <output name="tabular" file="survival_output.tabular" ftype="tabular" />
    </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 perform survival analysis for the identification of a pathogenicity score cut-off. Two input tabular files need to be provided, one containing VINIL scores and annotations on a cohort of affected individual, and one from a population of unaffected controls. Please be make sure that both files were obtained by applying the same scoring system that is, by running VINIL with the same parameters. Weird results might be obtained otherwise.

See the "survival" and the "VINYL-optimizer" utilities for the optimization of the score and the calculation of individual scores from a single vcf file.
A complete workflow that automates the exectuion of VINYL is available under the public workflows in the Galaxy VINYL instance
  </help>
  <citations>
  </citations>
</tool>