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comparison ensembl_vep.xml @ 1:27fd1c1f00a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ensembl_vep commit 1d05f91b90a92d0c6c60a635711704fe93e00562
author iuc
date Tue, 28 Jun 2022 10:41:15 +0000
parents 7303183cdb87
children b43df0ce6c87
comparison
equal deleted inserted replaced
0:7303183cdb87 1:27fd1c1f00a8
1 <tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@"> 1 <tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>with VEP</description> 2 <description>with VEP</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">106.1</token> 4 <token name="@TOOL_VERSION@">106.1</token>
5 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@DB_VERSION@">106</token> 6 <token name="@DB_VERSION@">106</token>
6 <xml name="vcf_input"> 7 <xml name="vcf_input">
7 <param type="data" name="input1" label="VCF input file" format="vcf"> 8 <param type="data" name="input1" label="VCF input file" format="vcf">
8 <validator type="unspecified_build" /> 9 <validator type="unspecified_build" />
9 <yield /> 10 <yield />
25 grep -v "#" '${annotation_cache.custom_annotation}' | 26 grep -v "#" '${annotation_cache.custom_annotation}' |
26 LC_ALL=C sort -k1,1 -k4,4n -k5,5n -t$'\t' | 27 LC_ALL=C sort -k1,1 -k4,4n -k5,5n -t$'\t' |
27 bgzip -c > 'custom_annotation.${custom_ext}.gz' && 28 bgzip -c > 'custom_annotation.${custom_ext}.gz' &&
28 tabix -p gff 'custom_annotation.${custom_ext}.gz' && 29 tabix -p gff 'custom_annotation.${custom_ext}.gz' &&
29 #end if 30 #end if
31 #if $ref_seq.ref_source == "cached":
32 ln -s '$ref_seq.ref.fields.path' reference.fa &&
33 #else if $ref_seq.ref_source == "history":
34 ln -s '$ref_seq.ref' reference.fa &&
35 #end if
36
30 vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf 37 vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf
31 #if $annotation_cache.source == "custom": 38 #if $annotation_cache.source == "custom":
32 --$custom_ext 'custom_annotation.${custom_ext}.gz' 39 --$custom_ext 'custom_annotation.${custom_ext}.gz'
33 #else: 40 #else:
34 --cache 41 --cache
38 #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged 45 #if $annotation_cache.cache_file.fields.cachetype == "merged": --merged
39 #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version 46 #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache_version $annotation_cache.cache_file.fields.version
40 ## The --offline flag automatically activates --cache. This is not wanted in our gff/gtf case but also not needed as no internet connection is required for annotating with these custom annotation sources. 47 ## The --offline flag automatically activates --cache. This is not wanted in our gff/gtf case but also not needed as no internet connection is required for annotating with these custom annotation sources.
41 --offline 48 --offline
42 #end if 49 #end if
43 #if $ref_seq.ref_source == "cached": 50 #if $ref_seq.ref_source != "no_ref"
44 --fasta '${ref_seq.ref.fields.path}' 51 --fasta reference.fa
45 #elif $ref_seq.ref_source == "history":
46 --fasta '${ref_seq.ref}'
47 #end if 52 #end if
48 --stats_text 53 --stats_text
49 54
50 #if $out_opt.sift != "None": --sift $out_opt.sift 55 #if $out_opt.sift != "None": --sift $out_opt.sift
51 #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen 56 #if $out_opt.polyphen != "None": --polyphen $out_opt.polyphen