# HG changeset patch
# User artbio
# Date 1613746605 0
# Node ID 9265faa93098aba502a4f28d0d1a6a9b2d68b6ba
# Parent  7421ab885b2797ad67971347966a20862d2eb6bd
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8-dirty"

diff -r 7421ab885b27 -r 9265faa93098 segmentation_sequenza.R
--- a/segmentation_sequenza.R	Thu Feb 18 19:03:54 2021 +0000
+++ b/segmentation_sequenza.R	Fri Feb 19 14:56:45 2021 +0000
@@ -42,9 +42,13 @@
 ## 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")
+
 segfile <- sequenza.extract(data_file,
-                            verbose = TRUE) # ,
-                            # chromosome.list = as.character(c(1:22)))
+                            verbose = TRUE,
+                            chromosome.list = chrom_list)
 
 ## Estimation of cellularity and ploidy
 
diff -r 7421ab885b27 -r 9265faa93098 snvtocnv.xml
--- a/snvtocnv.xml	Thu Feb 18 19:03:54 2021 +0000
+++ b/snvtocnv.xml	Fri Feb 19 14:56:45 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.1">
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2">
     <description>
     </description>
     <macros>
@@ -25,9 +25,9 @@
     #end if
     sequenza-utils gc_wiggle  --fasta reference.fa -o reference.gc50Base.wig.gz -w 50 &&
     sequenza-utils snp2seqz -v '$input_snvs'  -gc reference.gc50Base.wig.gz -o sample.seqz.gz &&
-    sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o sample.binned.seqz.gz &&
+    sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' &&
     Rscript $__tool_directory__/segmentation_sequenza.R
-            -i sample.binned.seqz.gz
+            -i '$wiggle'
             -s sample
             -O test &&
     Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
@@ -45,6 +45,7 @@
         </param>
     </inputs>
     <outputs>
+        <data name="wiggle" format="binary" label="binned wiggle" />
         <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" />