annotate gnali.xml @ 0:9ca12bc2be43 draft

"planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
author nml
date Mon, 30 Mar 2020 11:48:21 -0400
parents
children 3bfa1089a2c4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
1 <tool id="gnali" name="gNALI" version="0.1.0" python_template_version="3.6">
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
2 <description>Get nonessential, LoF variants</description>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
3 <requirements>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
4 <requirement type="package" version="0.1">gnali</requirement>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
5 </requirements>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
7 gnali -i '$test_genes' -o output
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
8 ]]></command>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
9 <inputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
10 <param type="data" name="test_genes" label="Test genes" format="txt" help="Specify a list of genes as HGNC symbols, separated by newline characters" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
11 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
12 <option value="gnomad2.1.1" selected="true">gnomAD2.1.1 (GRCh37/hg19)</option>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
13 </param>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
14 </inputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
15 <outputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
16 <data name="basic_output" label="gNALI basic output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
17 <data name="detailed_output" label="gNALI detailed output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
18 </outputs>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
19 <tests>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
20 <test>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
21 <param name="test_genes" value="test_genes.txt"/>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
22 <output name="basic_output">
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
23 <assert_contents>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
24 <has_text text="CCR5" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
25 </assert_contents>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
26 </output>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
27 <output name="detailed_output">
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
28 <assert_contents>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
29 <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
30 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
31 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
32 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
33 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
34 </assert_contents>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
35 </output>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
36 </test>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
37 </tests>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
38 <help><![CDATA[
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
39
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
40 gNALI - Gene Nonessentiality and Loss-of-function Identifier
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
41 ============================================================
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
42
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
43 gNALI is a tool to find (high confidence) potential loss-of-function variants of genes.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
44
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
45
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
46 Authors
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
47 -------
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
48
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
49 gNALI was developed by Xia Liu.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
50
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
51
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
52 Usage
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
53 -----
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
54
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
55 Accepted input formats: csv, txt, tsv
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
56
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
57 Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
58 It should not contain any blank lines until the end of the list.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
59
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
60 There will be two output files:
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
61
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
62 1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
63 2. A detailed output file, with more information on the variants.
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
64
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
65 ]]></help>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
66 <citations>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
67 <citation type="bibtex">
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
68 @misc{GitHubgnali,
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
69 author = {Xia, Liu},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
70 year = {2020},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
71 title = {gnali},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
72 publisher = {phac-nml},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
73 journal = {GitHub repository},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
74 url = {https://github.com/phac-nml/gnali/},
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
75 }</citation>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
76 </citations>
9ca12bc2be43 "planemo upload for repository https://github.com/phac-nml/gnali/ commit 1bb63f9b717c62189682e43098042852fceb4d43"
nml
parents:
diff changeset
77 </tool>