Mercurial > repos > artbio > snvtocnv
changeset 4:e299c477b475 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10edea05400e21ba43942bd0cc582153d60ae2d9"
| author | artbio |
|---|---|
| date | Sat, 20 Feb 2021 09:10:06 +0000 |
| parents | 15b26e44b18d |
| children | 604281aa5ad4 |
| files | macro.xml segmentation_sequenza.R sequenza_to_hrdtools_input.R snvtocnv.xml |
| diffstat | 4 files changed, 7 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- 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 '${reference_source.index.fields.path}' reference.fa && #end if ]]></token> @@ -16,7 +16,7 @@ <option value="history">Use a genome from history and build index</option> </param> <when value="cached"> - <param name="index" type="select" label="Using built-in genome" help="Select genome from the list"> + <param name="index" type="select" label="Using built-in genome" help="Select genome sorted and with chr prefix (chr1, chr2, ...)"> <options from_data_table="fasta_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" />
--- a/segmentation_sequenza.R Fri Feb 19 15:22:05 2021 +0000 +++ b/segmentation_sequenza.R Sat Feb 20 09:10:06 2021 +0000 @@ -42,7 +42,7 @@ ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22 message(sprintf("\nExtraction step for %s", data_file)) -chrom_list = c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", +chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22")
--- a/sequenza_to_hrdtools_input.R Fri Feb 19 15:22:05 2021 +0000 +++ b/sequenza_to_hrdtools_input.R Sat Feb 20 09:10:06 2021 +0000 @@ -30,8 +30,8 @@ opt <- parse_args(OptionParser(option_list = option_list), args = commandArgs(trailingOnly = TRUE)) -sequenza_data <- as.tibble(read.delim(opt$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])