# HG changeset patch # User iuc # Date 1759597478 0 # Node ID 3aae4f16ac9e33532d7c2359a7f00cc55f94498d # Parent c7275bd8b4d65ceeb98281508b8d4f0722a0f839 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5 diff -r c7275bd8b4d6 -r 3aae4f16ac9e snpEff.xml --- a/snpEff.xml Mon Nov 18 22:15:34 2024 +0000 +++ b/snpEff.xml Sat Oct 04 17:04:38 2025 +0000 @@ -4,7 +4,9 @@ snpEff_macros.xml - + + coreutils + @@ -47,15 +49,23 @@ #if $intervals ### fix this for multiple dataset input -interval intervals.bed #end if - #if $statsFile: - -stats '$statsFile' - #end if - #if $csvStats: - -csvStats '$csvFile' - #end if #if str($chr).strip() != '': -chr '$chr' #end if + #if $generate_stats or $generate_gene_stats or $csvStats: + #if $csvStats: + $csvStats snpeff_stats.csv + #end if + #if $generate_stats or ($generate_gene_stats and not $csvStats): + ## the base name passed in via the -csvStats or the -s option also determines the name of the genes.txt file + ## so in the absence of the first we need the second to have a consistent name of the genes.txt file + -s snpeff_stats.html + #end if + #else: + ## when no stats output is requested by the user, we can make things a little more efficient + ## by telling snpEff that it doesn't have to write even the default (html and genes.txt) ones. + -noStats + #end if $noLog ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes @@ -88,17 +98,15 @@ '$snpDb.genome_version' #end if '$input' > '$snpeff_output' - #if $statsFile: - && - #import os - #if $csvStats: - #set $genes_file = str($csvFile) + '.genes.txt' - #else - #set $genes_file = str($statsFile) + '.genes.txt' - #end if - #set $genes_file_name = os.path.split($genes_file)[-1] - mkdir '$statsFile.files_path' && - mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' + #if $generate_gene_stats: + ## remove the first, unnecessary comment line from the output + && tail -n+2 snpeff_stats.genes.txt > genes.txt + #end if + #if $generate_stats: + ## independently of whether the user asked for the gene.txt file, + ## we need to add it to files_path because the stats html report links to it. + && mkdir '$statsFile.files_path' && + mv snpeff_stats.genes.txt $statsFile.files_path #end if ]]> @@ -114,7 +122,8 @@ - + + @@ -127,14 +136,15 @@ - - + +
- + + @@ -142,7 +152,7 @@ - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" + value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@
@@ -160,7 +170,7 @@ - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" + value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@ @@ -188,7 +198,7 @@ - + @@ -328,22 +338,43 @@ - + generate_stats - + + generate_gene_stats + + csvStats + + + + + + + + + + + + + + + + + - - + + + + - @@ -356,14 +387,39 @@ + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + diff -r c7275bd8b4d6 -r 3aae4f16ac9e snpEff_create_db.xml --- a/snpEff_create_db.xml Mon Nov 18 22:15:34 2024 +0000 +++ b/snpEff_create_db.xml Sat Oct 04 17:04:38 2025 +0000 @@ -126,8 +126,10 @@ - - + + + + @@ -137,8 +139,10 @@ - - + + + + @@ -148,10 +152,14 @@ - - - - + + + + + + + + @@ -160,10 +168,14 @@ - - - - + + + + + + + + @@ -172,10 +184,14 @@ - - - - + + + + + + + + diff -r c7275bd8b4d6 -r 3aae4f16ac9e snpEff_download.xml --- a/snpEff_download.xml Mon Nov 18 22:15:34 2024 +0000 +++ b/snpEff_download.xml Sat Oct 04 17:04:38 2025 +0000 @@ -22,21 +22,20 @@ - - + + + + + 5.2 - 0 + 1 SnpEff5.2 + + ['SnpEff5.0', 'SnpEff5.1', 'SnpEff5.2'] + SnpEff 5.0 - 5.2 + + + snpeff diff -r c7275bd8b4d6 -r 3aae4f16ac9e snpeff_get_chr_names.xml --- a/snpeff_get_chr_names.xml Mon Nov 18 22:15:34 2024 +0000 +++ b/snpeff_get_chr_names.xml Sat Oct 04 17:04:38 2025 +0000 @@ -42,15 +42,15 @@ This can only be used on built-in databases manually configured by your galaxy admin. - - + + This can only be used on databases in your history that were downloaded using the snpEff download tool. - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" + value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@ @@ -62,7 +62,7 @@ This can only be used on databases in your history that were created using the snpEff build tool. - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" + value.metadata.snpeff_version in @COMPATIBLE_DB_VERSIONS@ @@ -72,18 +72,22 @@ - - + + + + - - + + - - + + + + + + key, version, value, name, path + +
+ + key, version, genome, value, name + +
+