Mercurial > repos > iuc > nextclade

comparison nextclade.xml @ 4:774876053025 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
author iuc
date Wed, 01 Sep 2021 17:54:55 +0000
parents 167e492b7ae2
children fc0f242f08f6
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3:167e492b7ae2 4:774876053025
1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> 1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2 <description></description> 2 <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@TOOL_VERSION@">1.2.3</token>
6 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
7 </macros> 6 </macros>
8 <requirements> 7 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
10 <requirement type="package">coreutils</requirement> 9 <requirement type="package">coreutils</requirement>
11 </requirements> 10 </requirements>
11 <version_command>nextclade --version-detailed</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" && 13 nextclade dataset get -n '${organism}' -o db &&
14 ln -s "\$DB_PATH" db &&
15 #set $input_qc_config = "db/qc.json" 14 #set $input_qc_config = "db/qc.json"
16 #set $input_root_seq = "db/reference.fasta" 15 #set $input_root_seq = "db/reference.fasta"
17 #set $input_tree = "db/tree.json" 16 #set $input_tree = "db/tree.json"
18 #set $input_gene_map = "db/genemap.gff" 17 #set $input_gene_map = "db/genemap.gff"
19 #set $input_pcr_primers = "db/primers.csv" 18 #set $input_pcr_primers = "db/primers.csv"
71 <option value="report_tsv" selected="true">Tabular format report</option> 70 <option value="report_tsv" selected="true">Tabular format report</option>
72 <option value="output_tree">Auspice v2 tree file (JSON format)</option> 71 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
73 <option value="output_fasta">Aligned sequences (FASTA format)</option> 72 <option value="output_fasta">Aligned sequences (FASTA format)</option>
74 </param> 73 </param>
75 <param name="include_header" type="boolean" label="Include header line in output file" 74 <param name="include_header" type="boolean" label="Include header line in output file"
76 truevalue="true" falsevalue="false" /> 75 truevalue="true" falsevalue="false" />
76 <param name="organism" type="select" label="Organism">
77 <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
78 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
79 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
80 <option value="flu_vic_ha">Influenza B Victoria HA</option>
81 <option value="flu_yam_ha">Influenza B Yamagata HA</option>
82 </param>
77 <conditional name="adv"> 83 <conditional name="adv">
78 <param name="advanced_options" type="select" label="Use advanced options" > 84 <param name="advanced_options" type="select" label="Use advanced options" >
79 <option value="yes">Yes</option> 85 <option value="yes">Yes</option>
80 <option value="no" selected="true">No</option> 86 <option value="no" selected="true">No</option>
81 </param> 87 </param>
110 </outputs> 116 </outputs>
111 <tests> 117 <tests>
112 <test expect_num_outputs="1"> 118 <test expect_num_outputs="1">
113 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 119 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
114 <param name="outputs" value="report_tsv" /> 120 <param name="outputs" value="report_tsv" />
121 <param name="organism" value="sars-cov-2" />
115 <output name="report_tsv"> 122 <output name="report_tsv">
116 <assert_contents> 123 <assert_contents>
117 <has_n_columns n="48" /> 124 <has_n_columns n="48" />
118 <has_text text="20A" /> 125 <has_text text="20A" />
119 </assert_contents> 126 </assert_contents>
120 </output> 127 </output>
121 </test> 128 </test>
122 <test expect_num_outputs="3"> 129 <test expect_num_outputs="3">
123 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 130 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
124 <param name="outputs" value="report_tsv,report_json,output_tree" /> 131 <param name="outputs" value="report_tsv,report_json,output_tree" />
132 <param name="organism" value="sars-cov-2" />
125 <output name="report_tsv"> 133 <output name="report_tsv">
126 <assert_contents> 134 <assert_contents>
127 <has_n_columns n="48" /> 135 <has_n_columns n="48" />
128 <has_text text="20A" /> 136 <has_text text="20A" />
129 </assert_contents> 137 </assert_contents>
140 </output> 148 </output>
141 </test> 149 </test>
142 <test expect_num_outputs="1"> 150 <test expect_num_outputs="1">
143 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 151 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
144 <param name="outputs" value="report_tsv" /> 152 <param name="outputs" value="report_tsv" />
153 <param name="organism" value="sars-cov-2" />
145 <conditional name="adv"> 154 <conditional name="adv">
146 <param name="advanced_options" value="yes" /> 155 <param name="advanced_options" value="yes" />
147 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> 156 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
148 </conditional> 157 </conditional>
149 <output name="report_tsv"> 158 <output name="report_tsv">