diff mutational_patterns.xml @ 11:7995a949189f draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 94919d0f442fe7059afa2e07898c149b126a5460"

--- a/mutational_patterns.xml	Mon Oct 19 23:34:58 2020 +0000
+++ b/mutational_patterns.xml	Thu Oct 22 00:18:38 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy11">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy12">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
@@ -47,9 +47,12 @@
     #end if
 
     #if $set_cosmic.choices == 'yes':
-        --cosmic_version $set_cosmic.cosmic_version
+        --cosmic_version '$set_cosmic.cosmic_version'
         --signum '$set_cosmic.signum'
         --output_cosmic $cosmic
+        #if $set_cosmic.contrib_matrix_out
+            --sig_contrib_matrix $sig_contrib_matrix
+        #end if
     #end if
             
     #if $rdata_out
@@ -129,6 +132,8 @@
                     <option value="v2" selected="true">Cosmic v2, March 2015</option>
                     <option value="v3">Cosmic v3, May 2019</option>
                 </param>
+                <param name="contrib_matrix_out" type="boolean" checked="false" label="Output Signature Contribution table ?"
+                       help="Output the normalized signatures contributions for further visualization" />
             </when>
              <when value="no" />
         </conditional>
@@ -147,6 +152,10 @@
         <data name="cosmic" format="pdf" label="Cosmic signatures">
             <filter>set_cosmic['choices'] == "yes"</filter>
         </data>
+        <data name="sig_contrib_matrix" format="tabular" label="${tool.name}: Signature contribution table">
+            <filter>set_cosmic['contrib_matrix_out']</filter>
+        </data>
+
         <data name="rdata" format="rdata" label="${tool.name}: RData file">
             <filter>rdata_out</filter>
         </data>
@@ -175,7 +184,7 @@
             <conditional name="set_cosmic">
                 <param name="choices" value="no"/>
             </conditional>
-            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size" ftype="pdf"/>
+            <output name="spectrum" file="spectrum_output1.pdf" compare="sim_size"/>
         </test>
 
          <!-- de novo signatures -->
@@ -202,8 +211,8 @@
             <param name="rank" value="4" />
             <param name="newsignum" value="4" />
             <param name="rdata_out" value="true" />
-            <output name="denovo" file="denovo_output1.pdf" compare="sim_size" ftype="pdf"/>
-            <output name="sigmatrix" file="sigmatrix.tab" ftype="tabular" compare="sim_size"/>
+            <output name="denovo" file="denovo_output1.pdf" compare="sim_size"/>
+            <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
             <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
         </test>
 
@@ -227,9 +236,11 @@
             </conditional>
             <conditional name="set_cosmic">
                 <param name="choices" value="yes"/>
+                <param name="contrib_matrix_out"  value="true" />
             </conditional>
             <param name="signum" value="3" />
-            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/>
+            <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size"/>
+            <output name="sig_contrib_matrix" file="sig_contrib_table.tsv" compare="sim_size"/>
         </test>
         <!-- cosmic signature on single sample -->
         <test>
@@ -249,7 +260,7 @@
                 <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"/>
+            <output name="cosmic" file="cosmic_output2.pdf" compare="sim_size" delta="50000"/>
         </test>
     </tests>
     <help>