annotate gnali.xml @ 4:b6e197aac430 draft

"planemo upload for repository https://github.com/phac-nml/gnali/ commit 8b9f79cbb46fb4c935cf2c81726f1d41eb69bcd8"
author nml
date Fri, 19 Mar 2021 13:29:55 +0000
parents 02d368ec14cf
children 65521c432f58
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
b6e197aac430 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 8b9f79cbb46fb4c935cf2c81726f1d41eb69bcd8"
nml
parents: 3
diff changeset
1 <tool id="gnali" name="gNALI" version="1.0.3" python_template_version="3.7">
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
2 <description>Get nonessential, LoF variants</description>
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
3 <macros>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
4 <import>macros.xml</import>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
5 </macros>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
6 <expand macro="requirements" />
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
8 gnali -i '$test_genes' -o output -d '$database_info.database'
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
9 #if $database_info.predefined_filters != "None":
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
10 --predefined_filters '$database_info.predefined_filters'
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
11 #end if
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
12 #if len($additional_filters) > 0:
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
13 --additional_filters
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
14 #for $filt in $additional_filters
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
15 '$filt.filter'
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
16 #end for
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
17 #end if
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
18 #if $vcf_output:
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
19 '$vcf_output'
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
20 #end if
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
21 #if $pop_freqs:
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
22 '$pop_freqs'
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
23 #end if
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
24 ]]></command>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
25 <inputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
26 <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" />
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
27 <param name="vcf_output" type="boolean" truevalue="--vcf" falsevalue="" optional="false" checked="false" label="VCF output" help="Generate vcf file for filtered variants" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
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" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
29 <conditional name="database_info">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
30 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
31 <option value="gnomadv2.1.1" selected="true">gnomADv2.1.1 (GRCh37/hg19)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
32 <option value="gnomadv3">gnomADv3 (GRCh38/hg38)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
33 </param>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
34 <when value="gnomadv2.1.1">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
35 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
36 <option value="homozygous-controls">homozygous controls (controls_nhomalt>0)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
37 <option value="heterozygous-controls">heterozygous controls (controls_nhomalt=0)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
38 <option value="nhomalt>0">homozygous (nhomalt>0)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
39 </param>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
40 </when>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
41 <when value="gnomadv3">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
42 <param name="predefined_filters" type="select" display="checkboxes" multiple="True" label="Predefined filters" help="Filter variants by selected filters">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
43 <option value="homozygous">homozygous (nhomalt>0)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
44 <option value="heterozygous">heterozygous (nhomalt=0)</option>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
45 </param>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
46 </when>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
47 </conditional>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
48 <repeat name="additional_filters" title="Additional filters" min="0" default="0" help="Additional filters (as expressions, ex. AC>10) to apply" >
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
49 <param name="filter" type="text" optional="False" label="Filter">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
50 <sanitizer invalid_char="">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
51 <valid initial="string.ascii_letters,string.digits">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
52 <add value="&gt;" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
53 <add value="&lt;" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
54 <add value="=" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
55 </valid>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
56 </sanitizer>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
57 </param>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
58 </repeat>
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
59 </inputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
60 <outputs>
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
61 <data name="basic_output" label="gNALI basic output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
62 <data name="detailed_output" label="gNALI detailed output on ${test_genes.element_identifier}" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
63 <data name="variants_vcf_output" label="gNALI variants vcf on ${test_genes.element_identifier}" format="vcf" from_work_dir="output/Nonessential_Gene_Variants.vcf" >
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
64 <filter>vcf_output</filter>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
65 </data>
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
66 </outputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
67 <tests>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
68 <test>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
69 <param name="test_genes" value="test_genes.txt"/>
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
70 <param name="predefined_filters" value="homozygous-controls"/>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
71 <param name="pop_freqs" value="--pop_freqs"/>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
72 <param name="vcf_output" value="--vcf"/>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
73 <output name="basic_output"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
74 value="results/Nonessential_Host_Genes_Basic.txt"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
75 ftype="txt"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
76 compare="diff">
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
77 </output>
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
78 <output name="detailed_output"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
79 value="results/Nonessential_Host_Genes_Detailed.txt"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
80 ftype="txt"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
81 compare="diff">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
82 </output>
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
83 <output name="variants_vcf_output"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
84 value="results/Nonessential_Gene_Variants.vcf"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
85 ftype="vcf"
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
86 compare="diff">
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
87 </output>
2
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
nml
parents: 1
diff changeset
88 </test>
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
89 </tests>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
90 <help><![CDATA[
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
91
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
92 Introduction
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
93 ------------------
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
94
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
95 gNALI (gene nonessentiality and loss-of-function identifier) is a tool to find (high confidence)
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
96 potential loss of function variants of genes.
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
97
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
98 NOTE: loss-of-function is influenced by the genome build. Not all variants available in gnomADv2.1.1 are
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
99 available in gnomADv3 and vice versa.
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
100
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
101 Usage
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
102 -----------
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
103
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
104 Your input file must be of format .csv, .txt, or tsv and should contain a list of genes
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
105 (as HGNC symbols) to test, separated by newline characters.
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
106 It should not contain any blank lines until the end of the list.
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
107
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
108
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
109 **Population Frequencies**
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
110
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
111 When using the population frequencies feature:
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
112
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
113 Per population group:
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
114
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
115 * AC denotes allele count
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
116
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
117 * AN denotes allele number
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
118
3
02d368ec14cf "planemo upload for repository https://github.com/phac-nml/gnali/ commit 48745557cc8e603b61ba1a78308f72562f559e59"
nml
parents: 2
diff changeset
119 * AF denotes allele frequency
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
120
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
121 ]]></help>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
122 <citations>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
123 <citation type="bibtex">
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
124 @misc{GitHubgnali,
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
125 author = {Xia, Liu},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
126 year = {2020},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
127 title = {gnali},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
128 publisher = {phac-nml},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
129 journal = {GitHub repository},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
130 url = {https://github.com/phac-nml/gnali/},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
131 }</citation>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
132 </citations>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
133 </tool>
2
49012f2b4c19 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 5c43f6f0a86589e95959c4d57b60305c8aba548d"
nml
parents: 1
diff changeset
134