Mercurial > repos > nml > gnali

comparison gnali.xml @ 0:9ca12bc2be43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
comparison
equal deleted inserted replaced
-1:000000000000 0:9ca12bc2be43
1 <tool id="gnali" name="gNALI" version="0.1.0" python_template_version="3.6">
2 <description>Get nonessential, LoF variants</description>
3 <requirements>
4 <requirement type="package" version="0.1">gnali</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 gnali -i '$test_genes' -o output
8 ]]></command>
9 <inputs>
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" />
11 <param type="select" name="database" label="Database" format="txt" help="Database to query" >
12 <option value="gnomad2.1.1" selected="true">gnomAD2.1.1 (GRCh37/hg19)</option>
13 </param>
14 </inputs>
15 <outputs>
16 <data name="basic_output" label="gNALI basic output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Basic\).txt" />
17 <data name="detailed_output" label="gNALI detailed output" format="txt" from_work_dir="output/Nonessential_Host_Genes_\(Detailed\).txt" />
18 </outputs>
19 <tests>
20 <test>
21 <param name="test_genes" value="test_genes.txt"/>
22 <output name="basic_output">
23 <assert_contents>
24 <has_text text="CCR5" />
25 </assert_contents>
26 </output>
27 <output name="detailed_output">
28 <assert_contents>
29 <has_text_matching expression="Chromosome\tPosition_Start\tRSID\tReference_Allele\tAlternate_Allele\tScore\tQuality\tLoF_Variant\tLoF_Annotation\tHGNC_Symbol\tEnsembl Code" />
30 <has_text_matching expression="3\t46414935\trs938517991\tAT\tA\t9974.16\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
31 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t74264261.52\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
32 <has_text_matching expression="3\t46415066\trs146972949\tC\tT\t120238.89\tPASS\tT\tstop_gained\tCCR5\tENSG00000160791" />
33 <has_text_matching expression="3\t46414943\trs775750898\tTACAGTCAGTATCAATTCTGGAAGAATTTCCAG\tT\t1947603.90\tPASS\t-\tframeshift_variant\tCCR5\tENSG00000160791" />
34 </assert_contents>
35 </output>
36 </test>
37 </tests>
38 <help><![CDATA[
39
40 gNALI - Gene Nonessentiality and Loss-of-function Identifier
41 ============================================================
42
43 gNALI is a tool to find (high confidence) potential loss-of-function variants of genes.
44
45
46 Authors
47 -------
48
49 gNALI was developed by Xia Liu.
50
51
52 Usage
53 -----
54
55 Accepted input formats: csv, txt, tsv
56
57 Your input file should contain a list of genes (as HGNC symbols) to test, separated by newline characters.
58 It should not contain any blank lines until the end of the list.
59
60 There will be two output files:
61
62 1. A basic output file, containing genes (as HGNC symbols) with nonessential, loss-of-function variants.
63 2. A detailed output file, with more information on the variants.
64
65 ]]></help>
66 <citations>
67 <citation type="bibtex">
68 @misc{GitHubgnali,
69 author = {Xia, Liu},
70 year = {2020},
71 title = {gnali},
72 publisher = {phac-nml},
73 journal = {GitHub repository},
74 url = {https://github.com/phac-nml/gnali/},
75 }</citation>
76 </citations>
77 </tool>