# HG changeset patch
# User artbio
# Date 1613812206 0
# Node ID e299c477b475d0a97c2ed461a5cd32f4a443a27f
# Parent  15b26e44b18d94ef3a9edd822f0a849ce11c82a3
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10edea05400e21ba43942bd0cc582153d60ae2d9"

diff -r 15b26e44b18d -r e299c477b475 macro.xml
--- a/macro.xml	Fri Feb 19 15:22:05 2021 +0000
+++ b/macro.xml	Sat Feb 20 09:10:06 2021 +0000
@@ -3,9 +3,9 @@
 
     <token name="@set_fasta_index@"><![CDATA[
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s '${reference_source.ref_file}' reference.fa &&
+        cp '${reference_source.ref_file}' reference.fa &&
     #else:
-        ln -s '${reference_source.index.fields.path}' reference.fa &&
+        cp '${reference_source.index.fields.path}' reference.fa &&
     #end if
     ]]></token>
 
@@ -16,7 +16,7 @@
                 <option value="history">Use a genome from history and build index</option>
             </param>
             <when value="cached">
-                <param name="index" type="select" label="Using built-in genome" help="Select genome from the list">
+                <param name="index" type="select" label="Using built-in genome" help="Select genome sorted and with chr prefix (chr1, chr2, ...)">
                     <options from_data_table="fasta_indexes">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No indexes are available" />
diff -r 15b26e44b18d -r e299c477b475 segmentation_sequenza.R
--- a/segmentation_sequenza.R	Fri Feb 19 15:22:05 2021 +0000
+++ b/segmentation_sequenza.R	Sat Feb 20 09:10:06 2021 +0000
@@ -42,7 +42,7 @@
 ## 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",
+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")
 
diff -r 15b26e44b18d -r e299c477b475 sequenza_to_hrdtools_input.R
--- a/sequenza_to_hrdtools_input.R	Fri Feb 19 15:22:05 2021 +0000
+++ b/sequenza_to_hrdtools_input.R	Sat Feb 20 09:10:06 2021 +0000
@@ -30,8 +30,8 @@
 opt <- parse_args(OptionParser(option_list = option_list),
                  args = commandArgs(trailingOnly = TRUE))
 
-sequenza_data <- as.tibble(read.delim(opt$input, header = TRUE))
-solutions_data <- as.tibble(read.delim(opt$solutions, header = TRUE))
+sequenza_data <- as_tibble(read.delim(opt$input, header = TRUE))
+solutions_data <- as_tibble(read.delim(opt$solutions, header = TRUE))
 
 
 ploidy <- round(solutions_data$ploidy[1])
diff -r 15b26e44b18d -r e299c477b475 snvtocnv.xml
--- a/snvtocnv.xml	Fri Feb 19 15:22:05 2021 +0000
+++ b/snvtocnv.xml	Sat Feb 20 09:10:06 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2.1">
+<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.3.0">
     <description>
     </description>
     <macros>