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comparison nextclade.xml @ 0:919cc9dc23f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
author iuc
date Mon, 26 Apr 2021 19:08:26 +0000
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children 495c19a62538
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-1:000000000000 0:919cc9dc23f0
1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@TOOL_VERSION@">0.14.2</token>
6 <token name="@VERSION_SUFFIX@">0</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 nextclade
13 --input-fasta '${input_fasta}'
14 #if $outputs and "report_tsv" in $outputs
15 --output-tsv '${report_tsv}'
16 #end if
17 #if $outputs and "report_json" in $outputs
18 --output-json '${report_json}'
19 #end if
20 #if $outputs and "output_tree" in $outputs
21 --output-tree '${output_tree}'
22 #end if
23 #if str($adv.advanced_options) == "yes"
24 #if $adv.input_qc_config
25 --input-qc-config '${adv.input_qc_config}'
26 #end if
27 #if $adv.input_root_seq
28 --input-root-seq '${adv.input_root_seq}'
29 #end if
30 #if $adv.input_tree
31 --input-tree '${adv.input_tree}'
32 #end if
33 #if $adv.input_gene_map
34 --input-gene-map '${adv.input_gene_map}'
35 #end if
36 #if $adv.input_pcr_primers
37 --input-pcr-primers '${adv.input_pcr_primers}'
38 #end if
39 #end if
40 ]]></command>
41 <inputs>
42 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" />
43 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
44 <option value="report_json">JSON format report</option>
45 <option value="report_tsv" selected="true">Tabular format report</option>
46 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
47 </param>
48 <conditional name="adv">
49 <param name="advanced_options" type="select" label="Use advanced options" >
50 <option value="yes">Yes</option>
51 <option value="no" selected="true">No</option>
52 </param>
53 <when value="yes">
54 <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" />
55 <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" />
56 <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" />
57 <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" />
58 <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" />
59 </when>
60 <when value="no">
61 </when>
62 </conditional>
63 </inputs>
64 <outputs>
65 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
66 <filter>outputs and "report_tsv" in outputs</filter>
67 </data>
68 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
69 <filter>outputs and "report_json" in outputs</filter>
70 </data>
71 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
72 <filter>outputs and "output_tree" in outputs</filter>
73 </data>
74 </outputs>
75 <tests>
76 <test expect_num_outputs="1">
77 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
78 <param name="outputs" value="report_tsv" />
79 <output name="report_tsv">
80 <assert_contents>
81 <has_text text="20A" />
82 </assert_contents>
83 </output>
84 </test>
85 <test expect_num_outputs="3">
86 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
87 <param name="outputs" value="report_tsv,report_json,output_tree" />
88 <output name="report_tsv">
89 <assert_contents>
90 <has_text text="20A" />
91 </assert_contents>
92 </output>
93 <output name="report_json">
94 <assert_contents>
95 <has_text text='"pos": 240,' />
96 </assert_contents>
97 </output>
98 <output name="output_tree">
99 <assert_contents>
100 <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' />
101 </assert_contents>
102 </output>
103 </test>
104 <test expect_num_outputs="1">
105 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
106 <param name="outputs" value="report_tsv" />
107 <conditional name="adv">
108 <param name="advanced_options" value="yes" />
109 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
110 </conditional>
111 <output name="report_tsv">
112 <assert_contents>
113 <has_text text="mediocre" />
114 </assert_contents>
115 </output>
116 </test>
117 </tests>
118 <help><![CDATA[
119
120 .. class:: infomark
121
122 **What it does**
123
124 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
125
126 **Input**
127
128 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
129
130 **Output**
131
132 Outputs can include:
133
134 * A tabular format file with a report, one line per input sequence
135
136 * A JSON format file with the same information as is present in the tabular report
137
138 * An Auspice v2 tree file in JSON format
139
140 .. _Nextclade: https://github.com/nextstrain/nextclade
141
142 ]]></help>
143 <expand macro="citations" />
144 </tool>