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comparison datasets_genome.xml @ 13:d979ba07ddd4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
author iuc
date Mon, 21 Nov 2022 11:39:29 +0000
parents e8d51503c749
children a222b4d3d52e
comparison
equal deleted inserted replaced
12:e8d51503c749 13:d979ba07ddd4
13 #else 13 #else
14 --inputfile '$query.subcommand.text_or_file.inputfile' 14 --inputfile '$query.subcommand.text_or_file.inputfile'
15 #end if 15 #end if
16 #else: 16 #else:
17 '$query.subcommand.taxon' 17 '$query.subcommand.taxon'
18 $query.subcommand.tax_exact_match
18 #end if 19 #end if
19 $filters.reference 20 $filters.reference
20 $filters.annotated 21 $filters.annotated
21 #if $filters.assembly_level: 22 #if $filters.assembly_level:
22 --assembly-level $filters.assembly_level 23 --assembly-level $filters.assembly_level
23 #end if 24 #end if
25 --assembly-version $filters.assembly_version
24 #if $filters.assembly_source: 26 #if $filters.assembly_source:
25 --assembly-source $filters.assembly_source 27 --assembly-source $filters.assembly_source
26 #end if 28 #end if
27 #if $filters.chromosomes: 29 #if $filters.chromosomes:
28 --chromosomes '$filters.chromosomes' 30 --chromosomes '$filters.chromosomes'
29 #end if 31 #end if
30 @EXCLUDES_GENOME@ 32 $filters.exclude_atypical
31 @INCLUDES_GENOME@ 33 @INCLUDE@
32 @RELEASED_BEFORE@ 34 @RELEASED_BEFORE@
33 @RELEASED_SINCE@ 35 @RELEASED_AFTER@
34 #for search_term in $filters.search: 36 #for search_term in $filters.search:
35 --search '$filters.search_term' 37 --search '$filters.search_term'
36 #end for 38 #end for
39 --no-progressbar
37 #if $uncompressed 40 #if $uncompressed
38 && 7z x -y ncbi_dataset.zip 41 && 7z x -y ncbi_dataset.zip
39 #else 42 #else
40 && 7z l ncbi_dataset.zip > ncbi_dataset.txt 43 && 7z l ncbi_dataset.zip > ncbi_dataset.txt
41 #end if 44 #end if
49 </param> 52 </param>
50 <when value="accession"> 53 <when value="accession">
51 <expand macro="text_or_file"/> 54 <expand macro="text_or_file"/>
52 </when> 55 </when>
53 <when value="taxon"> 56 <when value="taxon">
54 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."></param> 57 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."/>
58 <param argument="--tax-exact-match" type="boolean" truevalue="--tax-exact-match" falsevalue="" label="Exclude sub-species when a species-level taxon is specified"/>
55 </when> 59 </when>
56 </conditional> 60 </conditional>
57 </section> 61 </section>
58 <section name="filters" title="Filters and Limit"> 62 <section name="filters" title="Filters and Limit">
59 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/> 63 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
60 <expand macro="annotation"></expand> 64 <expand macro="annotation"/>
61 <expand macro="assembly_level"></expand> 65 <expand macro="assembly_level"/>
62 <expand macro="assembly_source"></expand> 66 <param argument="--assembly-version" type="select" label="Assembly version(s)">
63 <expand macro="chromosomes"></expand> 67 <option value="latest">Latest</option>
64 <expand macro="released_options"></expand> 68 <option value="all">All</option>
65 <expand macro="released_options" before_or_after="since"></expand> 69 </param>
70 <!-- TODO add test for assembly source: according to CLI doc args are RefSeq, GenBank, All and not refseq / genbank-->
71 <expand macro="assembly_source"/>
72 <expand macro="chromosomes"/>
73 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/>
74 <expand macro="released_options"/>
75 <expand macro="released_options" before_or_after="after"/>
66 76
67 <repeat name="search" title="Add search terms"> 77 <repeat name="search" title="Add search terms">
68 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/> 78 <param argument="--search" type="text" label="Only include genomes that have the specified text in the searchable fields" help="Searchable fields are species and infraspecies, assembly name and submitter"/>
69 </repeat> 79 </repeat>
70 </section> 80 </section>
71 <section name="file_choices" title="File Choices" expanded="true"> 81 <section name="file_choices" title="File Choices" expanded="true">
72 <expand macro="excludes_genome"></expand> 82 <expand macro="include"/>
73 <expand macro="includes_genome"></expand>
74 </section> 83 </section>
75 <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/> 84 <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/>
76 </inputs> 85 </inputs>
77 <outputs> 86 <outputs>
78 <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip"> 87 <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip">
83 </data> 92 </data>
84 <data name="genome_data_report" format="json" label="NCBI Genome Datasets: Data Report" from_work_dir="ncbi_dataset/data/assembly_data_report.jsonl"> 93 <data name="genome_data_report" format="json" label="NCBI Genome Datasets: Data Report" from_work_dir="ncbi_dataset/data/assembly_data_report.jsonl">
85 <filter>uncompressed</filter> 94 <filter>uncompressed</filter>
86 </data> 95 </data>
87 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list"> 96 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
88 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 97 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
89 <filter>uncompressed</filter> 98 <filter>uncompressed and file_choices['include'] and "seq-report" in file_choices['include']</filter>
90 </collection> 99 </collection>
91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list"> 100 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
92 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)\.(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 101 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
93 <filter>uncompressed and not file_choices['exclude_seq']</filter> 102 <filter>uncompressed and file_choices['include'] and "genome" in file_choices['include']</filter>
103 </collection>
104 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
105 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
106 <filter>uncompressed and file_choices['include'] and "rna" in file_choices['include']</filter>
107 </collection>
108 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
109 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
110 <filter>uncompressed and file_choices['include'] and "protein" in file_choices['include']</filter>
94 </collection> 111 </collection>
95 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list"> 112 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
96 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 113 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
97 <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter> 114 <filter>uncompressed and file_choices['include'] and "cds" in file_choices['include']</filter>
98 </collection> 115 </collection>
99 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list"> 116 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
100 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 117 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
101 <filter>uncompressed and not file_choices['exclude_gff3']</filter> 118 <filter>uncompressed and file_choices['include'] and "gff3" in file_choices['include']</filter>
102 </collection> 119 </collection>
103 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list"> 120 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
104 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 121 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
105 <filter>uncompressed and not file_choices['exclude_rna']</filter> 122 <filter>uncompressed and file_choices['include'] and "gtf" in file_choices['include']</filter>
106 </collection>
107 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
108 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
109 <filter>uncompressed and not file_choices['exclude_protein']</filter>
110 </collection> 123 </collection>
111 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list"> 124 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
112 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 125 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
113 <filter>uncompressed and file_choices['include_gbff']</filter> 126 <filter>uncompressed and file_choices['include'] and "gbff" in file_choices['include']</filter>
114 </collection>
115 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
116 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
117 <filter>uncompressed and file_choices['include_gtf']</filter>
118 </collection> 127 </collection>
119 </outputs> 128 </outputs>
120 <tests> 129 <tests>
121 <test expect_num_outputs="2"> 130 <test expect_num_outputs="2">
122 <conditional name="query|subcommand"> 131 <conditional name="query|subcommand">
123 <param name="download_by" value="taxon"></param> 132 <param name="download_by" value="taxon"/>
124 <param name="text_or_file" value="text"></param> 133 <param name="text_or_file" value="text"/>
125 <param name="taxon" value="human"></param> 134 <param name="taxon" value="human"/>
126 </conditional> 135 </conditional>
127 <param name="chromosomes" value="21"></param> 136 <param name="chromosomes" value="21"/>
128 <param name="exclude_protein" value="true"/> 137 <param name="include" value=""/>
129 <param name="exclude_rna" value="true"/>
130 <param name="exclude_seq" value="true"/>
131 <param name="exclude_genomic_cds" value="true"/>
132 <param name="exclude_gff3" value="true"/>
133 <param name="uncompressed" value="false"/> 138 <param name="uncompressed" value="false"/>
134 <param name="released_before" value="01/01/2018"></param> 139 <param name="released_before" value="01/01/2018"/>
135 <output name="archive_contents"> 140 <output name="archive_contents">
136 <assert_contents> 141 <assert_contents>
137 <has_text text="ncbi_dataset/data/dataset_catalog.json"/> 142 <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
138 </assert_contents> 143 </assert_contents>
139 </output> 144 </output>
140 </test> 145 </test>
141 <test expect_num_outputs="2"> 146 <test expect_num_outputs="2">
142 <conditional name="query|subcommand"> 147 <conditional name="query|subcommand">
143 <param name="download_by" value="taxon"></param> 148 <param name="download_by" value="taxon"/>
144 <param name="text_or_file" value="text"></param> 149 <param name="text_or_file" value="text"/>
145 <param name="taxon" value="human"></param> 150 <param name="taxon" value="human"/>
146 </conditional> 151 </conditional>
147 <param name="chromosomes" value="21"></param> 152 <param name="chromosomes" value="21"/>
148 <param name="uncompressed" value="false"/> 153 <param name="include" value="genome"/>
149 <param name="exclude_protein" value="true"/> 154 <param name="uncompressed" value="true"/>
150 <param name="exclude_rna" value="true"/> 155 <param name="assembly_level" value="chromosome,complete"/>
151 <param name="exclude_seq" value="true"/> 156 <param name="released_before" value="01/01/2018"/>
152 <param name="exclude_genomic_cds" value="true"/> 157 <output_collection name="genome_fasta" type="list:list" count="14">
153 <param name="exclude_gff3" value="true"/> 158 <expand macro="genome_fasta_assert" el1="GCA_000002115.2" el2="chr21" expression=">"/>
154 <param name="assembly_level" value="chromosome"/> 159 <expand macro="genome_fasta_assert" el1="GCA_000002125.2" el2="chr21" expression=">"/>
155 <param name="released_before" value="01/01/2018"></param> 160 <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/>
156 <output name="archive_contents"> 161 <expand macro="genome_fasta_assert" el1="GCA_000212995.1" el2="chr21" expression=">"/>
157 <assert_contents> 162 <expand macro="genome_fasta_assert" el1="GCA_000252825.1" el2="chr21" expression=">"/>
158 <has_text text="ncbi_dataset/data/dataset_catalog.json"/> 163 <expand macro="genome_fasta_assert" el1="GCA_000306695.2" el2="chr21" expression=">"/>
164 <expand macro="genome_fasta_assert" el1="GCA_000365445.1" el2="chr21" expression=">"/>
165 <!-- TODO chromosomes argument (or data) seems not reliable https://github.com/ncbi/datasets/issues/188-->
166 <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/>
167 <expand macro="genome_fasta_assert" el1="GCA_001292825.2" el2="chr21" expression=">"/>
168 <expand macro="genome_fasta_assert" el1="GCA_001524155.4" el2="chr21" expression=">"/>
169 <expand macro="genome_fasta_assert" el1="GCA_001712695.1" el2="chr21" expression=">"/>
170 <expand macro="genome_fasta_assert" el1="GCA_022833125.2" el2="chr21" expression=">"/>
171 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
172 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
173 </output_collection>
174 <output name="genome_data_report">
175 <assert_contents>
176 <has_text text="Homo sapiens"/>
177 </assert_contents>
178 </output>
179 </test>
180 <!-- same as precious test but assembly_source (refseq which removes some of the genomes) -->
181 <test expect_num_outputs="2">
182 <conditional name="query|subcommand">
183 <param name="download_by" value="taxon"/>
184 <param name="text_or_file" value="text"/>
185 <param name="taxon" value="human"/>
186 </conditional>
187 <param name="chromosomes" value="21"/>
188 <param name="include" value="genome"/>
189 <param name="uncompressed" value="true"/>
190 <param name="assembly_level" value="chromosome,complete"/>
191 <param name="assembly_source" value="refseq"/>
192 <param name="released_before" value="01/01/2018"/>
193 <output_collection name="genome_fasta" type="list:list" count="2">
194 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
195 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
196 </output_collection>
197 <output name="genome_data_report">
198 <assert_contents>
199 <has_text text="Homo sapiens"/>
159 </assert_contents> 200 </assert_contents>
160 </output> 201 </output>
161 </test> 202 </test>
162 <test expect_num_outputs="4"> 203 <test expect_num_outputs="4">
163 <conditional name="query|subcommand"> 204 <conditional name="query|subcommand">
164 <param name="download_by" value="accession"></param> 205 <param name="download_by" value="accession"/>
165 <conditional name="text_or_file"> 206 <conditional name="text_or_file">
166 <param name="text_or_file" value="text"></param> 207 <param name="text_or_file" value="text"/>
167 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"></param> 208 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"/>
168 </conditional> 209 </conditional>
169 </conditional> 210 </conditional>
170 <param name="uncompressed" value="true"/> 211 <param name="include" value="seq-report,gtf,cds"/>
171 <param name="released_before" value="01/01/2007"></param> 212 <param name="uncompressed" value="true"/>
172 <param name="exclude_protein" value="true"/> 213 <param name="released_before" value="01/01/2007"/>
173 <param name="exclude_rna" value="true"/>
174 <param name="exclude_seq" value="true"/>
175 <param name="exclude_gff3" value="true"/>
176 <param name="include_gtf" value="true"/>
177 <output name="genome_data_report"> 214 <output name="genome_data_report">
178 <assert_contents> 215 <assert_contents>
179 <has_text text="GCF_000013305.1"/> 216 <has_text text="GCF_000013305.1"/>
180 </assert_contents> 217 </assert_contents>
181 </output> 218 </output>
188 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/> 225 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
189 </output_collection> 226 </output_collection>
190 </test> 227 </test>
191 <test expect_num_outputs="4"> 228 <test expect_num_outputs="4">
192 <conditional name="query|subcommand"> 229 <conditional name="query|subcommand">
193 <param name="download_by" value="accession"></param> 230 <param name="download_by" value="accession"/>
194 <conditional name="text_or_file"> 231 <conditional name="text_or_file">
195 <param name="text_or_file" value="file"></param> 232 <param name="text_or_file" value="file"/>
196 <param name="inputfile" value="accessions.txt"></param> 233 <param name="inputfile" value="accessions.txt"/>
197 </conditional> 234 </conditional>
198 </conditional> 235 </conditional>
199 <param name="include_gbff" value="true"/> 236 <param name="include" value="seq-report,gbff,gff3"/>
200 <param name="exclude_protein" value="true"/> 237 <param name="uncompressed" value="true"/>
201 <param name="exclude_rna" value="true"/> 238 <param name="released_before" value="01/01/2007"/>
202 <param name="exclude_seq" value="true"/>
203 <param name="exclude_genomic_cds" value="true"/>
204 <param name="uncompressed" value="true"/>
205 <param name="released_before" value="01/02/2007"></param>
206 <output name="genome_data_report"> 239 <output name="genome_data_report">
207 <assert_contents> 240 <assert_contents>
208 <has_text text="SAMN02604181"/> 241 <has_text text="SAMN02604181"/>
209 </assert_contents> 242 </assert_contents>
210 </output> 243 </output>
217 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/> 250 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
218 </output_collection> 251 </output_collection>
219 </test> 252 </test>
220 <test expect_num_outputs="2"> 253 <test expect_num_outputs="2">
221 <conditional name="query|subcommand"> 254 <conditional name="query|subcommand">
222 <param name="download_by" value="accession"></param> 255 <param name="download_by" value="accession"/>
223 <conditional name="text_or_file"> 256 <conditional name="text_or_file">
224 <param name="text_or_file" value="text"></param> 257 <param name="text_or_file" value="text"/>
225 <param name="accession" value="GCF_000001405.40"></param> 258 <param name="accession" value="GCF_000001405"/>
226 </conditional> 259 </conditional>
227 </conditional> 260 </conditional>
228 <param name="exclude_protein" value="true"/> 261 <param name="include" value="seq-report"/>
229 <param name="exclude_rna" value="true"/> 262 <param name="uncompressed" value="true"/>
230 <param name="exclude_seq" value="true"/> 263 <param name="released_before" value="01/01/2015"/>
231 <param name="exclude_genomic_cds" value="true"/> 264 <param name="assembly_version" value="all"/>
232 <param name="exclude_gff3" value="true"/> 265 <output_collection name="sequence_report" count="4">
233 <param name="uncompressed" value="true"/> 266 <element name="GCF_000001405.25">
234 <param name="released_before" value="01/02/2007"></param>
235 <output_collection name="sequence_report">
236 <element name="GCF_000001405.40">
237 <assert_contents> 267 <assert_contents>
238 <has_text text="assignedMoleculeLocationType"/> 268 <has_text text="assignedMoleculeLocationType"/>
239 </assert_contents> 269 </assert_contents>
240 </element> 270 </element>
271 <element name="GCF_000001405.26">
272 <assert_contents>
273 <has_text text="assignedMoleculeLocationType"/>
274 </assert_contents>
275 </element>
276 <element name="GCF_000001405.27">
277 <assert_contents>
278 <has_text text="assignedMoleculeLocationType"/>
279 </assert_contents>
280 </element>
281 <element name="GCF_000001405.28">
282 <assert_contents>
283 <has_text text="assignedMoleculeLocationType"/>
284 </assert_contents>
285 </element>
241 </output_collection> 286 </output_collection>
242 </test> 287 </test>
243 <test expect_num_outputs="5"> 288 <test expect_num_outputs="5">
244 <conditional name="query|subcommand"> 289 <conditional name="query|subcommand">
245 <param name="download_by" value="accession"></param> 290 <param name="download_by" value="accession"/>
246 <conditional name="text_or_file"> 291 <conditional name="text_or_file">
247 <param name="text_or_file" value="text"></param> 292 <param name="text_or_file" value="text"/>
248 <param name="accession" value="GCF_000146045.2"></param> 293 <param name="accession" value="GCF_000146045.2"/>
249 </conditional> 294 </conditional>
250 </conditional> 295 </conditional>
251 <param name="exclude_protein" value="true"/> 296 <param name="include" value="seq-report,genome,rna,cds"/>
252 <param name="exclude_rna" value="false"/>
253 <param name="exclude_seq" value="false"/>
254 <param name="exclude_genomic_cds" value="false"/>
255 <param name="exclude_gff3" value="true"/>
256 <param name="uncompressed" value="true"/> 297 <param name="uncompressed" value="true"/>
257 <output_collection name="genome_fasta" type="list:list" count="1"> 298 <output_collection name="genome_fasta" type="list:list" count="1">
258 <element name="GCF_000146045.2"> 299 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
259 <element name="chrI">
260 <assert_contents>
261 <has_text text=">NC_001133.9"/>
262 </assert_contents>
263 </element>
264 </element>
265 </output_collection> 300 </output_collection>
266 </test> 301 </test>
267 <test expect_num_outputs="3"> 302 <test expect_num_outputs="3">
268 <conditional name="query|subcommand"> 303 <conditional name="query|subcommand">
269 <param name="download_by" value="accession"></param> 304 <param name="download_by" value="accession"/>
270 <conditional name="text_or_file"> 305 <conditional name="text_or_file">
271 <param name="text_or_file" value="text"></param> 306 <param name="text_or_file" value="text"/>
272 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"></param> 307 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"/>
273 </conditional> 308 </conditional>
274 </conditional> 309 </conditional>
275 <param name="exclude_protein" value="true"/> 310 <param name="include" value="seq-report,genome"/>
276 <param name="exclude_rna" value="true"/>
277 <param name="exclude_seq" value="false"/>
278 <param name="exclude_genomic_cds" value="true"/>
279 <param name="exclude_gff3" value="true"/>
280 <param name="uncompressed" value="true"/> 311 <param name="uncompressed" value="true"/>
281 <output_collection name="genome_fasta" type="list:list" count="2"> 312 <output_collection name="genome_fasta" type="list:list" count="2">
282 <element name="GCF_000002945.1"> 313 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/>
283 <element name="chrI"> 314 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
284 <assert_contents> 315 </output_collection>
285 <has_text text=">NC_003424.3"/> 316 </test>
286 </assert_contents> 317 <!-- tax_exact_match seems not able to filter out strains
287 </element> 318 https://github.com/ncbi/datasets/issues/187
288 </element> 319 hence we set expect_test_failure="true"-->
289 <element name="GCF_000146045.2"> 320 <test expect_num_outputs="1" expect_test_failure="true">
290 <element name="chrI"> 321 <conditional name="query|subcommand">
291 <assert_contents> 322 <param name="download_by" value="taxon"/>
292 <has_text text=">NC_001133.9"/> 323 <param name="text_or_file" value="text"/>
293 </assert_contents> 324 <param name="taxon" value="4932"/>
294 </element> 325 <param name="tax_exact_match" value="true"/>
295 </element> 326 </conditional>
296 </output_collection> 327 <param name="include" value=""/>
328 <param name="uncompressed" value="true"/>
329 <output name="genome_data_report">
330 <assert_contents>
331 <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>
332 </assert_contents>
333 </output>
297 </test> 334 </test>
298 </tests> 335 </tests>
299 <help> 336 <help>
300 <![CDATA[ 337 <![CDATA[
301 **Download Genome Datasets from NCBI** 338 **Download Genome Datasets from NCBI**