Mercurial > repos > iuc > ensembl_vep
changeset 1:27fd1c1f00a8 draft
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 |
| files | ensembl_vep.xml |
| diffstat | 1 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/ensembl_vep.xml Wed May 11 13:03:38 2022 +0000 +++ b/ensembl_vep.xml Tue Jun 28 10:41:15 2022 +0000 @@ -1,7 +1,8 @@ -<tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@"> +<tool id="ensembl_vep" name="Predict variant effects" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>with VEP</description> <macros> <token name="@TOOL_VERSION@">106.1</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@DB_VERSION@">106</token> <xml name="vcf_input"> <param type="data" name="input1" label="VCF input file" format="vcf"> @@ -27,6 +28,12 @@ bgzip -c > 'custom_annotation.${custom_ext}.gz' && tabix -p gff 'custom_annotation.${custom_ext}.gz' && #end if + #if $ref_seq.ref_source == "cached": + ln -s '$ref_seq.ref.fields.path' reference.fa && + #else if $ref_seq.ref_source == "history": + ln -s '$ref_seq.ref' reference.fa && + #end if + vep -i '${annotation_cache.input1}' -o MainOutput.vcf --vcf #if $annotation_cache.source == "custom": --$custom_ext 'custom_annotation.${custom_ext}.gz' @@ -40,10 +47,8 @@ ## 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. --offline #end if - #if $ref_seq.ref_source == "cached": - --fasta '${ref_seq.ref.fields.path}' - #elif $ref_seq.ref_source == "history": - --fasta '${ref_seq.ref}' + #if $ref_seq.ref_source != "no_ref" + --fasta reference.fa #end if --stats_text