# HG changeset patch
# User artbio
# Date 1652992473 0
# Node ID f3bacfd9b67027fa00007e330a3a9f5d27f56cae
# Parent  67213c4eefa6b041df2f95ff244c5f83290944c1
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688

diff -r 67213c4eefa6 -r f3bacfd9b670 segmentation_sequenza.R
--- a/segmentation_sequenza.R	Sun Mar 07 23:13:08 2021 +0000
+++ b/segmentation_sequenza.R	Thu May 19 20:34:33 2022 +0000
@@ -40,9 +40,9 @@
 ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22
 message(sprintf("\nExtraction step for %s", data_file))
 
-chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
-               "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
-               "chr18", "chr19", "chr20", "chr21", "chr22")
+  chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
+                "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17",
+                "chr18", "chr19", "chr20", "chr21", "chr22", "chrX")
 
 Sys.setenv(TZDIR = "/usr/share/zoneinfo/")
 Sys.setenv(TZ = "US/Eastern")
diff -r 67213c4eefa6 -r f3bacfd9b670 snvtocnv.xml
--- a/snvtocnv.xml	Sun Mar 07 23:13:08 2021 +0000
+++ b/snvtocnv.xml	Thu May 19 20:34:33 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0">
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy0">
     <description>
     </description>
     <macros>
@@ -26,7 +26,8 @@
     Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
             -i test/sample_segments.txt
             -s test/sample_alternative_solutions.txt
-            -o '$cnvs'
+            -o '$cnvs' &&
+    ls test
     ]]></command>
     <inputs>
         <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/>
@@ -37,17 +38,32 @@
         <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" />
         <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
         <data name="cnvs" format="tabular" label="Annotated CNVs" />
+        <data name="chrom_depths" format="pdf" label="Chromosomes sequencing depth" from_work_dir="test/sample_chromosome_depths.pdf"/>
+        <data name="chrom_view" format="pdf" label="Chromosomes views" from_work_dir="test/sample_chromosome_view.pdf"/>
+        <data name="genome_view" format="pdf" label="Genome view" from_work_dir="test/sample_genome_view.pdf"/>        
+        <data name="model_fit" format="pdf" label="Cellularity and Diploidy model" from_work_dir="test/sample_model_fit.pdf"/>        
+        <data name="CN_histo" format="pdf" label="Copy Numbers histogram" from_work_dir="test/sample_CN_bars.pdf"/>        
     </outputs>
     <tests>
         <test>
             <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" />
             <param name="refwig" value="hg19.GCref.txt" />
             <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" />
+            <output name="chrom_depths" ftype="pdf" file="hg19_chrom_depths.pdf"/>
+            <output name="chrom_view" ftype="pdf" file="hg19_chrom_view.pdf"/>
+            <output name="genome_view" ftype="pdf" file="hg19_genome_view.pdf"/>        
+            <output name="model_fit" ftype="pdf" file="hg19_model.pdf"/>        
+            <output name="CN_histo" ftype="pdf" file="hg19_CN_histo.pdf"/>        
         </test>
         <test>
             <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" />
             <param name="refwig" value="hg38.GCref.txt" />
             <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" />
+            <output name="chrom_depths" ftype="pdf" file="hg38_chrom_depths.pdf"/>
+            <output name="chrom_view" ftype="pdf" file="hg38_chrom_view.pdf"/>
+            <output name="genome_view" ftype="pdf" file="hg38_genome_view.pdf"/>        
+            <output name="model_fit" ftype="pdf" file="hg38_model.pdf"/>        
+            <output name="CN_histo" ftype="pdf" file="hg38_CN_histo.pdf"/>        
         </test>
     </tests>
     <help>
diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg19_CN_histo.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg19_chrom_depths.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg19_chrom_view.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg19_genome_view.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg19_model.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg38_CN_histo.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg38_chrom_depths.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg38_chrom_view.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg38_genome_view.pdf
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diff -r 67213c4eefa6 -r f3bacfd9b670 test-data/hg38_model.pdf
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