# HG changeset patch # User jjohnson # Date 1460217100 14400 # Node ID 924af057bbcaeb8a64f5e346b3a31a07340b9dde # Parent bb0797deab7878a31da4023661c3aa704661cebf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty diff -r bb0797deab78 -r 924af057bbca snpEff.xml --- a/snpEff.xml Wed Dec 09 10:20:13 2015 -0500 +++ b/snpEff.xml Sat Apr 09 11:51:40 2016 -0400 @@ -8,33 +8,30 @@ $snpeff_output ; + "$input" > "$snpeff_output"; #if $statsFile: #import os #set $genes_file = str($statsFile) + '.genes.txt' #set $genes_file_name = os.path.split($genes_file)[-1] mkdir $statsFile.files_path; - mv $genes_file #echo os.path.join($statsFile.files_path, $genes_file_name)#; + mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; #end if #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" - sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' $snpeff_output + sed -i -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output" #end if ]]> @@ -213,12 +210,6 @@ - - - - - - @@ -257,9 +248,9 @@ - + - + @@ -313,7 +304,7 @@ ^\S*$ - + @@ -344,7 +335,6 @@ - @@ -362,27 +352,6 @@ - - - - - - - - - - - - - - - - - - - @@ -406,7 +375,6 @@ - @@ -424,8 +392,6 @@ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - ]]> diff -r bb0797deab78 -r 924af057bbca snpEff_databases.xml --- a/snpEff_databases.xml Wed Dec 09 10:20:13 2015 -0500 +++ b/snpEff_databases.xml Sat Apr 09 11:51:40 2016 -0400 @@ -8,7 +8,7 @@ $snpeff_dbs + java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs" ]]> @@ -16,13 +16,21 @@ + + + + + + + + + + diff -r bb0797deab78 -r 924af057bbca snpEff_download.xml --- a/snpEff_download.xml Wed Dec 09 10:20:13 2015 -0500 +++ b/snpEff_download.xml Sat Apr 09 11:51:40 2016 -0400 @@ -8,7 +8,7 @@ @@ -20,12 +20,20 @@ + + + + + + + + + + diff -r bb0797deab78 -r 924af057bbca snpEff_genes.txt --- a/snpEff_genes.txt Wed Dec 09 10:20:13 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3455 +0,0 @@ -# The following table is formatted as tab separated values. -#GeneName GeneId TranscriptId BioType variants_impact_HIGH variants_impact_LOW variants_impact_MODERATE variants_impact_MODIFIER variants_effect_3_prime_UTR_variant variants_effect_5_prime_UTR_premature_start_codon_gain_variant variants_effect_5_prime_UTR_variant variants_effect_disruptive_inframe_deletion variants_effect_disruptive_inframe_deletion+splice_region_variant variants_effect_disruptive_inframe_insertion variants_effect_downstream_gene_variant variants_effect_frameshift_variant variants_effect_frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant variants_effect_frameshift_variant+splice_region_variant variants_effect_frameshift_variant+start_lost variants_effect_frameshift_variant+stop_gained variants_effect_frameshift_variant+stop_lost variants_effect_inframe_deletion variants_effect_inframe_deletion+splice_region_variant variants_effect_inframe_insertion variants_effect_intron_variant variants_effect_missense_variant variants_effect_missense_variant+splice_region_variant variants_effect_non_coding_exon_variant variants_effect_sequence_feature variants_effect_splice_acceptor_variant+intron_variant variants_effect_splice_acceptor_variant+splice_region_variant+intron_variant variants_effect_splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant variants_effect_splice_donor_variant+intron_variant variants_effect_splice_region_variant variants_effect_splice_region_variant+intron_variant variants_effect_splice_region_variant+non_coding_exon_variant variants_effect_splice_region_variant+stop_retained_variant variants_effect_splice_region_variant+synonymous_variant variants_effect_start_lost variants_effect_stop_gained variants_effect_stop_gained+splice_region_variant variants_effect_stop_lost variants_effect_stop_retained_variant variants_effect_synonymous_variant variants_effect_upstream_gene_variant bases_affected_DOWNSTREAM total_score_DOWNSTREAM length_DOWNSTREAM bases_affected_EXON total_score_EXON length_EXON bases_affected_INTRON total_score_INTRON length_INTRON bases_affected_NONE total_score_NONE length_NONE bases_affected_SPLICE_SITE_ACCEPTOR total_score_SPLICE_SITE_ACCEPTOR length_SPLICE_SITE_ACCEPTOR bases_affected_SPLICE_SITE_DONOR total_score_SPLICE_SITE_DONOR length_SPLICE_SITE_DONOR bases_affected_SPLICE_SITE_REGION total_score_SPLICE_SITE_REGION length_SPLICE_SITE_REGION bases_affected_TRANSCRIPT total_score_TRANSCRIPT length_TRANSCRIPT bases_affected_UPSTREAM total_score_UPSTREAM length_UPSTREAM bases_affected_UTR_3_PRIME total_score_UTR_3_PRIME length_UTR_3_PRIME 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -AC002059.10 ENSG00000273216 ENST00000608014 sense_intronic 0 0 0 8 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 5000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -AC002472.1 ENSG00000269103 ENST00000547793 protein_coding 0 0 0 29 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 29 0 5000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -AC002472.11 ENSG00000226872 ENST00000450652 antisense 0 0 0 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0 0 3 0 147 14 0 11199 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 5000 0 0 0 0 0 0 -AC004019.13 ENSG00000236754 ENST00000443935 antisense 0 1 0 34 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 15 0 0 4 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 13 2 0 5000 4 0 1326 15 0 5494 0 0 0 0 0 0 0 0 0 1 0 6 0 0 0 13 0 5000 0 0 0 0 0 0 -AC004461.4 ENSG00000237347 ENST00000412461 processed_pseudogene 0 0 0 3 0 0 0 0 0 0 3 0 0 0 0 0 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processed_pseudogene 0 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 5000 0 0 0 0 0 0 -AC005399.1 ENSG00000269774 ENST00000600045 pseudogene 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 5000 0 0 0 0 0 0 -AC006547.13 ENSG00000236540 ENST00000415503 antisense 0 0 0 17 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 5000 0 0 0 13 0 1992 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -AC006547.13 ENSG00000236540 ENST00000595864 antisense 0 0 0 17 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 5000 0 0 0 13 0 2017 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -AC006547.13 ENSG00000236540 ENST00000596334 antisense 0 0 0 17 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 5000 0 0 0 13 0 1995 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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