Mercurial > repos > iuc > nextclade

annotate nextclade.xml @ 9:d070e316da5d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e768bff1262aadb15a58680fed83636562171c05"
author iuc
date Mon, 15 Nov 2021 18:57:23 +0000
parents 56b1a13d9680
children 64be7ff9b97b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
2 <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
3 <macros>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
3
3b75d5285aff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 7a13866c45dba2337fc37d66c45c77ac73915690"
iuc
parents: 2
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
6 </macros>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
7 <requirements>
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
6
1e0234b87809 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 475d00042b5ec4216fa1e5f52e3ec0cf25c67707"
iuc
parents: 5
diff changeset
9 <requirement type="package" version="8.31">coreutils</requirement>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
10 </requirements>
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
11 <version_command>nextclade --version-detailed</version_command>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
13 nextclade dataset get -n '${organism}' -o db &&
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
14 #set $input_qc_config = "db/qc.json"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
15 #set $input_root_seq = "db/reference.fasta"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
16 #set $input_tree = "db/tree.json"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
17 #set $input_gene_map = "db/genemap.gff"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
18 #set $input_pcr_primers = "db/primers.csv"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
19 #if str($adv.advanced_options) == "yes"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
20 #if $adv.input_qc_config
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
21 #set $input_qc_config = $adv.input_qc_config
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
22 #end if
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
23 #if $adv.input_root_seq
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
24 #set $input_root_seq = $adv.input_root_seq
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
25 #end if
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
26 #if $adv.input_tree
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
27 #set $input_tree = $adv.input_tree
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
28 #end if
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
29 #if $adv.input_gene_map
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
30 #set $input_gene_map = $adv.input_gene_map
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
31 #end if
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
32 #if $adv.input_pcr_primers
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
33 #set $input_pcr_primers = $adv.input_pcr_primers
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
34 #end if
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
35 #end if
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
36 nextclade
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
37 --input-fasta '${input_fasta}'
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
38 --input-qc-config '${input_qc_config}'
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
39 --input-root-seq '${input_root_seq}'
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
40 --input-tree '${input_tree}'
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
41 --input-gene-map '${input_gene_map}'
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
42 --input-pcr-primers '${input_pcr_primers}'
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
43 #if $outputs and "report_tsv" in $outputs
2
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
44 #if $include_header
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
45 --output-tsv '$report_tsv'
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
46 #else
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
47 --output-tsv report.tsv
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
48 #end if
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
49 #end if
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
50 #if $outputs and "report_json" in $outputs
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
51 --output-json '${report_json}'
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
52 #end if
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
53 #if $outputs and "output_tree" in $outputs
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
54 --output-tree '${output_tree}'
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
55 #end if
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
56 #if $outputs and "output_fasta" in $outputs
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
57 --output-fasta "${output_fasta}"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
58 #if str($adv.advanced_options) == "yes"
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
59 $adv.include_reference
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
60 #end if
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
61 #end if
2
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
62 #if $outputs and "report_tsv" in $outputs and not $include_header
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
63 && tail -n+2 report.tsv >'$report_tsv'
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
64 #end if
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
65 ]]></command>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
66 <inputs>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
67 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
68 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
69 <option value="report_json">JSON format report</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
70 <option value="report_tsv" selected="true">Tabular format report</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
71 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
72 <option value="output_fasta">Aligned sequences (FASTA format)</option>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
73 </param>
2
6cd62b6d2b5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents: 1
diff changeset
74 <param name="include_header" type="boolean" label="Include header line in output file"
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
75 truevalue="true" falsevalue="false" />
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
76 <param name="organism" type="select" label="Organism">
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
77 <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
78 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
79 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
80 <option value="flu_vic_ha">Influenza B Victoria HA</option>
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
81 <option value="flu_yam_ha">Influenza B Yamagata HA</option>
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
82 </param>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
83 <conditional name="adv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
84 <param name="advanced_options" type="select" label="Use advanced options" >
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
85 <option value="yes">Yes</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
86 <option value="no" selected="true">No</option>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
87 </param>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
88 <when value="yes">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
89 <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
90 <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
91 <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
92 <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
93 <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" />
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
94 <param argument="--include-reference" name="include_reference" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
95 </when>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
96 <when value="no">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
97 </when>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
98 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
99 </inputs>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
100 <outputs>
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
101 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
102 <filter>outputs and "report_tsv" in outputs</filter>
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
103 <actions>
7
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
iuc
parents: 6
diff changeset
104 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,frameShifts,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" />
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents: 0
diff changeset
105 </actions>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
106 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
107 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
108 <filter>outputs and "report_json" in outputs</filter>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
109 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
110 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
111 <filter>outputs and "output_tree" in outputs</filter>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
112 </data>
4
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
113 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)">
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
114 <filter>outputs and "output_fasta" in outputs</filter>
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents: 3
diff changeset
115 </data>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
116 </outputs>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
117 <tests>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
118 <test expect_num_outputs="1">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
119 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
120 <param name="outputs" value="report_tsv" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
121 <param name="organism" value="sars-cov-2" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
122 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
123 <assert_contents>
8
56b1a13d9680 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 9e5f2fc04f61230208adf2e321ce84cb66e86006"
iuc
parents: 7
diff changeset
124 <has_n_columns n="53" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
125 <has_text text="20A" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
126 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
127 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
128 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
129 <test expect_num_outputs="3">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
130 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
131 <param name="outputs" value="report_tsv,report_json,output_tree" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
132 <param name="organism" value="sars-cov-2" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
133 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
134 <assert_contents>
8
56b1a13d9680 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 9e5f2fc04f61230208adf2e321ce84cb66e86006"
iuc
parents: 7
diff changeset
135 <has_n_columns n="53" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
136 <has_text text="20A" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
137 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
138 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
139 <output name="report_json">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
140 <assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
141 <has_text text='"pos": 240,' />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
142 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
143 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
144 <output name="output_tree">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
145 <assert_contents>
7
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
iuc
parents: 6
diff changeset
146 <has_text text='"title": "QC Status"' />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
147 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
148 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
149 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
150 <test expect_num_outputs="1">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
151 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
152 <param name="outputs" value="report_tsv" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
153 <param name="organism" value="sars-cov-2" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
154 <conditional name="adv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
155 <param name="advanced_options" value="yes" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
156 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
157 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
158 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
159 <assert_contents>
8
56b1a13d9680 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 9e5f2fc04f61230208adf2e321ce84cb66e86006"
iuc
parents: 7
diff changeset
160 <has_n_columns n="53" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
161 <has_text text="mediocre" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
162 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
163 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
164 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
165 </tests>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
166 <help><![CDATA[
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
167
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
168 .. class:: infomark
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
169
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
170 **What it does**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
171
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
172 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
173
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
174 **Input**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
175
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
176 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
177
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
178 **Output**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
179
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
180 Outputs can include:
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
181
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
182 * A tabular format file with a report, one line per input sequence
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
183
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
184 * A JSON format file with the same information as is present in the tabular report
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
185
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
186 * An Auspice v2 tree file in JSON format
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
187
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
188 .. _Nextclade: https://github.com/nextstrain/nextclade
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
189
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
190 ]]></help>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
191 <expand macro="citations" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
192 </tool>