Mercurial > repos > artbio > mutational_patterns

diff mutational_patterns.xml @ 4:7ba08c826888 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit e2d6ed12516e1bd24071962a0dfe0220cc348f3c"
author artbio
date Mon, 05 Oct 2020 19:29:42 +0000
parents e332cf9dfa06
children fe31d059a482
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--- a/mutational_patterns.xml	Thu Sep 24 01:32:52 2020 +0000
+++ b/mutational_patterns.xml	Mon Oct 05 19:29:42 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy4">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy5">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
@@ -218,7 +218,7 @@
                 </collection>
             </param>
             <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
-            <param name="levels" value="GH_levels.tab" ftype="tabular"/>
+            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
             <conditional name="set_spectrum">
                 <param name="choices" value="no"/>
             </conditional>
@@ -231,6 +231,25 @@
             <param name="signum" value="3" />
             <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
         </test>
+        <test>
+            <param name="vcfs">
+                <collection type="list">
+                    <element name="1" value="G.vcf"/>
+                </collection>
+            </param>
+            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
+            <conditional name="set_spectrum">
+                <param name="choices" value="no"/>
+            </conditional>
+            <conditional name="set_denovo">
+                <param name="choices" value="no"/>
+            </conditional>
+            <conditional name="set_cosmic">
+                <param name="choices" value="yes"/>
+            </conditional>
+            <param name="signum" value="5" />
+            <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000" ftype="pdf"/>
+        </test>
     </tests>
     <help>