Mercurial > repos > elixir-it > vinyl_optimizer

comparison optimizer_genetic.xml @ 2:6e4eb4856874 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 22 Jul 2020 19:20:30 +0000
parents 35c308dd6420
children 221db2eb3c8e
comparison
equal deleted inserted replaced
1:35c308dd6420 2:6e4eb4856874
4 <requirement type="package" >perl</requirement> 4 <requirement type="package" >perl</requirement>
5 <requirement type="package" >r-base</requirement> 5 <requirement type="package" >r-base</requirement>
6 <requirement type="package" >r-genalg</requirement> 6 <requirement type="package" >r-genalg</requirement>
7 </requirements> 7 </requirements>
8 <command> <![CDATA[ 8 <command> <![CDATA[
9 ln -s $__tool_directory__/score_complete_alt_M.pl && 9 ln -s $__tool_directory__/score_complete_alt_M.pl 2>$log &&
10 ln -s $__tool_directory__/GENEO_VINYL.R && 10 ln -s $__tool_directory__/GENEO_VINYL.R 2>> $log &&
11 ln -s $fileR fileR && 11 ln -s $fileR fileR &&
12 ln -s $fileC fileC && 12 ln -s $fileC fileC &&
13 13
14 14
15 15
83 83
84 -XL $XL 84 -XL $XL
85 85
86 ###OUTPUT 86 ###OUTPUT
87 -ofile $ofile 87 -ofile $ofile
88
89 2>>$log
90 88
89 2>>$log
91 90
92 91
93 92
94 ]]> 93 ]]>
95 </command> 94 </command>
140 139
141 <!--others--> 140 <!--others-->
142 141
143 </inputs> 142 </inputs>
144 <outputs> 143 <outputs>
144 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
145 <data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/> 145 <data format="tsv" name="ofile" label="${tool.name} on ${on_string}: tsv "/>
146 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
147 </outputs> 146 </outputs>
148 <stdio> 147 <stdio>
149 </stdio> 148 </stdio>
150 <tests> 149 <tests>
151 <test> 150 <test>
152 <param name="fileR" value="TSI_annotated.vcf" ftype="vcf" /> 151 </test>
153 <param name="fileC" value="sorrentino_annotated.vcf" ftype="vcf" />
154 <param name="lgenes" value="DCM_genes.tabular" ftype="tabular" />
155 <param name="qfile" value="qfile.txt" ftype="txt" />
156 <param name="kfile" value="kfile.txt" ftype="txt" />
157 <param name="efile" value="efile.txt" ftype="txt" />
158 <param name="sfile" value="sfile.txt" ftype="txt" />
159 <output name="ofile" file="output_optimizer.tsv" ftype="tsv" />
160 <output name="log" file="log.txt" ftype="txt" />
161 </test>
162 </tests> 152 </tests>
163 <help> 153 <help>
164 **What it does** 154 **What it does**
165 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. 155 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.
166 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. 156 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.