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comparison gnali.xml @ 6:d1085589a5a7 draft

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"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
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5:65521c432f58 6:d1085589a5a7
1 <tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7"> 1 <tool id="gnali" name="gNALI" version="@VERSION@" python_template_version="3.7" profile="@PROFILE_VERSION@">
2 <description>Get nonessential, LoF variants</description> 2 <description>Get and filter nonessential, loss-of-function variants</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
27 <param name="vcf_output" type="boolean" truevalue="--vcf" falsevalue="" optional="false" checked="false" label="VCF output" help="Generate vcf file for filtered variants" /> 27 <param name="vcf_output" type="boolean" truevalue="--vcf" falsevalue="" optional="false" checked="false" label="VCF output" help="Generate vcf file for filtered variants" />
28 <param name="pop_freqs" type="boolean" truevalue="--pop_freqs" falsevalue="" optional="false" checked="false" label="Population frequencies" help="Generate population frequency data for variants that passed filtering" /> 28 <param name="pop_freqs" type="boolean" truevalue="--pop_freqs" falsevalue="" optional="false" checked="false" label="Population frequencies" help="Generate population frequency data for variants that passed filtering" />
29 <conditional name="database_info"> 29 <conditional name="database_info">
30 <param type="select" name="database" label="Database" format="txt" help="Database to query" > 30 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
31 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option> 31 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option>
32 <option value="gnomadv3">gnomADv3 (GRCh38/hg38)</option> 32 <option value="gnomadv3.1.1">gnomADv3.1.1 (GRCh38/hg38)</option>
33 </param> 33 </param>
34 <when value="gnomadv2.1.1"> 34 <when value="gnomadv2.1.1">
35 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> 35 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
36 <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option> 36 <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option>
37 <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option> 37 <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option>
38 <option value="nhomalt>0">homozygous (nhomalt>0)</option> 38 <option value="homozygous">homozygous (nhomalt>0)</option>
39 </param> 39 </param>
40 </when> 40 </when>
41 <when value="gnomadv3"> 41 <when value="gnomadv3.1.1">
42 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters"> 42 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
43 <option value="homozygous">homozygous (nhomalt>0)</option> 43 <option value="homozygous">homozygous (nhomalt>0)</option>
44 <option value="heterozygous">heterozygous (nhomalt=0)</option> 44 <option value="heterozygous">heterozygous (nhomalt=0)</option>
45 </param> 45 </param>
46 </when> 46 </when>
94 94
95 gNALI (gene nonessentiality and loss-of-function identifier) is a tool to find (high confidence) 95 gNALI (gene nonessentiality and loss-of-function identifier) is a tool to find (high confidence)
96 potential loss of function variants of genes. 96 potential loss of function variants of genes.
97 97
98 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are 98 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are
99 available in gnomADv3 and vice versa. 99 available in gnomADv3.1.1 and vice versa.
100 100
101 Usage 101 Usage
102 ----------- 102 -----------
103 103
104 Your input file must be of format .csv, .txt, or tsv and should contain a list of genes 104 Your input file must be of format .csv, .txt, or tsv and should contain a list of genes