diff mutational_patterns.xml @ 15:8182d1625433 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"

--- a/mutational_patterns.xml	Fri Jun 04 22:35:48 2021 +0000
+++ b/mutational_patterns.xml	Sun Oct 03 09:29:04 2021 +0000
@@ -1,13 +1,13 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy14">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy0">
     <description>from genomic variations in vcf files</description>
     <requirements>
-        <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>
-        <requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
-        <requirement type="package" version="0.2.20=r40h0357c0b_1002">r-rjson</requirement>
-        <requirement type="package" version="0.21.0=r40h0357c0b_1004">r-nmf</requirement>
-        <requirement type="package" version="2.3=r40h6115d3f_1003">r-gridextra</requirement>
-        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
-        <requirement type="package" version="1.4.3=r40_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
+        <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
+        <requirement type="package" version="1.6.6=r41hc72bb7e_1">r-optparse</requirement>
+        <requirement type="package" version="0.2.20=r41h03ef668_1002">r-rjson</requirement>
+        <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
+        <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
+        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
+        <requirement type="package" version="1.4.3=r41hdfd78af_3">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
 <!--
         <requirement type="package" version="1.3.1000=r40_4">bioconductor-bsgenome.hsapiens.ncbi.grch38</requirement>
         <requirement type="package" version="0.99.1=r40_4">bioconductor-bsgenome.hsapiens.1000genomes.hs37d5</requirement>
@@ -54,7 +54,7 @@
         --cosmic_version '$set_cosmic.cosmic_version'
         --signum '$set_cosmic.signum'
         --output_cosmic $cosmic
-        #if $set_cosmic.contrib_matrix_out
+        #if $set_cosmic.contrib_matrix_out == 'yes'
             --sig_contrib_matrix $sig_contrib_matrix
         #end if
     #end if
@@ -124,7 +124,7 @@
         </conditional>
 
         <conditional name="set_cosmic">
-            <param name="choices" type="select" label="Decompose with Cosmic signature v2" display="radio">
+            <param name="choices" type="select" label="Decompose with Cosmic signatures" display="radio">
                 <option value="yes" selected="true">Yes</option>
                 <option value="no">No</option>
             </param>
@@ -136,8 +136,11 @@
                     <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" />
+                <param name="contrib_matrix_out" type="select" label="Output Signature Contribution table ?"
+                       help="Output the normalized signatures contributions for further visualization" >
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
             </when>
              <when value="no" />
         </conditional>
@@ -157,7 +160,7 @@
             <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>
+            <filter>set_cosmic['choices'] == "yes" and set_cosmic['contrib_matrix_out'] == "yes"</filter>
         </data>
 
         <data name="rdata" format="rdata" label="${tool.name}: RData file">
@@ -166,6 +169,82 @@
 
     </outputs>
     <tests>
+         <!-- cosmic signatures with cosmic V3 -->
+        <test>
+            <param name="vcfs">
+                <collection type="list">
+                    <element name="6" value="F.vcf"/>
+                    <element name="7" value="G.vcf"/>
+                    <element name="8" value="H.vcf"/>
+                    <element name="9" value="I.vcf"/>
+                </collection>
+            </param>
+            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
+            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
+            <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"/>
+                <param name="contrib_matrix_out"  value="yes" />
+                <param name="cosmic_version" value="v3"/>
+            </conditional>
+            <param name="signum" value="3" />
+            <output name="cosmic" file="cosmic_output_v3.pdf" compare="sim_size"/>
+            <output name="sig_contrib_matrix" file="sig_contrib_table_v3.tsv" compare="sim_size"/>
+        </test>
+
+         <!-- cosmic signatures -->
+        <test>
+            <param name="vcfs">
+                <collection type="list">
+                    <element name="6" value="F.vcf"/>
+                    <element name="7" value="G.vcf"/>
+                    <element name="8" value="H.vcf"/>
+                    <element name="9" value="I.vcf"/>
+                </collection>
+            </param>
+            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
+            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
+            <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"/>
+                <param name="contrib_matrix_out"  value="yes" />
+            </conditional>
+            <param name="signum" value="3" />
+            <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>
+            <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"/>
+        </test>
+
         <!-- simple profile -->
         <test>
             <param name="vcfs">
@@ -219,53 +298,6 @@
             <output name="sigmatrix" file="sigmatrix.tab" compare="sim_size"/>
             <output name="rdata" file="denovo_1.RData" compare="sim_size" delta="400000"/> <!--  delta="170000" -->
         </test>
-
-         <!-- cosmic signatures -->
-        <test>
-            <param name="vcfs">
-                <collection type="list">
-                    <element name="6" value="F.vcf"/>
-                    <element name="7" value="G.vcf"/>
-                    <element name="8" value="H.vcf"/>
-                    <element name="9" value="I.vcf"/>
-                </collection>
-            </param>
-            <param name="genome" value="BSgenome.Hsapiens.UCSC.hg38"/>
-            <param name="levels" value="FGHI_levels.tab" ftype="tabular"/>
-            <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"/>
-                <param name="contrib_matrix_out"  value="true" />
-            </conditional>
-            <param name="signum" value="3" />
-            <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>
-            <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"/>
-        </test>
     </tests>
     <help>