comparison optimizer_genetic.xml @ 3:221db2eb3c8e draft default tip

Uploaded

2:6e4eb4856874

    <requirement type="package" >perl</requirement>
    <requirement type="package" >r-base</requirement>
    <requirement type="package" >r-genalg</requirement>
  </requirements>
  <command> <![CDATA[
	ln -s $__tool_directory__/score_complete_alt_M.pl 2>$log &&
	ln -s $__tool_directory__/GENEO_VINYL.R 2>> $log &&
	ln -s $fileR fileR &&
	ln -s $fileC fileC &&
	

	
	-XL $XL 
	
	###OUTPUT
	-ofile $ofile
 	
	2>>$log



    ]]>
  </command>

<!--others-->

  </inputs>
  <outputs>
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
    <data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/>
  </outputs>
  <stdio>
  </stdio>
  <tests>
      <test>
      </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.

3:221db2eb3c8e

    <requirement type="package" >perl</requirement>
    <requirement type="package" >r-base</requirement>
    <requirement type="package" >r-genalg</requirement>
  </requirements>
  <command> <![CDATA[
	ln -s $__tool_directory__/score_complete_alt_M.pl  &&
	ln -s $__tool_directory__/GENEO_VINYL.R  &&
	ln -s $fileR fileR &&
	ln -s $fileC fileC &&
	

	
	-XL $XL 
	
	###OUTPUT
	-ofile $ofile

        2>>$log
 	



    ]]>
  </command>

<!--others-->

  </inputs>
  <outputs>
    <data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/>
    <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
  </outputs>
  <stdio>
  </stdio>
  <tests>
    <test>
      <param name="fileR" value="TSI_annotated.vcf" ftype="vcf" />
      <param name="fileC" value="sorrentino_annotated.vcf" ftype="vcf" />
      <param name="lgenes" value="DCM_genes.tabular" ftype="tabular" />
      <param name="qfile" value="qfile.txt" ftype="txt" />
      <param name="kfile" value="kfile.txt" ftype="txt" />
      <param name="efile" value="efile.txt" ftype="txt" />
      <param name="sfile" value="sfile.txt" ftype="txt" />
      <output name="ofile" file="output_optimizer.tsv" ftype="tsv" />
      <output name="log" file="log.txt" ftype="txt" />
    </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.