Mercurial > repos > nml > gnali
changeset 6:d1085589a5a7 draft
"planemo upload for repository https://github.com/phac-nml/gnali/ commit 8779aba2c77e9ed7364c91e04a75b9c3468b7143"
author | nml |
---|---|
date | Fri, 11 Jun 2021 21:08:17 +0000 |
parents | 65521c432f58 |
children | 2b1154ae7e21 |
files | gnali.xml macros.xml test-data/results/Nonessential_Host_Genes_Basic.txt test-data/test_genes.txt |
diffstat | 4 files changed, 12 insertions(+), 10 deletions(-) [+] |
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--- a/gnali.xml Tue May 04 15:13:43 2021 +0000 +++ b/gnali.xml Fri Jun 11 21:08:17 2021 +0000 @@ -1,5 +1,5 @@ -<tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7"> - <description>Get nonessential, LoF variants</description> +<tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7" profile="@PROFILE_VERSION@"> + <description>Get and filter nonessential, loss-of-function variants</description> <macros> <import>macros.xml</import> </macros> @@ -29,16 +29,16 @@ <conditional name="database_info"> <param type="select" name="database" label="Database" format="txt" help="Database to query" > <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option> - <option value="gnomadv3">gnomADv3 (GRCh38/hg38)</option> + <option value="gnomadv3.1.1">gnomADv3.1.1 (GRCh38/hg38)</option> </param> <when value="gnomadv2.1.1"> <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option> <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option> - <option value="nhomalt>0">homozygous (nhomalt>0)</option> + <option value="homozygous">homozygous (nhomalt>0)</option> </param> </when> - <when value="gnomadv3"> + <when value="gnomadv3.1.1"> <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> <option value="homozygous">homozygous (nhomalt>0)</option> <option value="heterozygous">heterozygous (nhomalt=0)</option> @@ -96,7 +96,7 @@ potential loss of function variants of genes. NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are -available in gnomADv3 and vice versa. +available in gnomADv3.1.1 and vice versa. Usage -----------
--- a/macros.xml Tue May 04 15:13:43 2021 +0000 +++ b/macros.xml Fri Jun 11 21:08:17 2021 +0000 @@ -1,5 +1,6 @@ <macros> - <token name="@VERSION@">1.0.4</token> + <token name="@VERSION@">1.0.5</token> + <token name="@PROFILE_VERSION@">20.01</token> <xml name="requirements"> <requirements> <requirement type="package" version ="@VERSION@">gnali</requirement>