Mercurial > repos > iuc > nextclade
comparison nextclade.xml @ 5:0c46b95d60c3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
author | iuc |
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date | Wed, 01 Sep 2021 17:56:32 +0000 |
parents | b74b9a7b3e3b |
children | 1e0234b87809 |
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4:b74b9a7b3e3b | 5:0c46b95d60c3 |
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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"> |