Mercurial > repos > iuc > ncbi_datasets

comparison datasets_genome.xml @ 8:b2ae7186d41f 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/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
author iuc
date Thu, 23 Jun 2022 17:33:12 +0000
parents 0622d99c2619
children 18eed8fa7f23
comparison
equal deleted inserted replaced
7:0622d99c2619 8:b2ae7186d41f
33 @RELEASED_SINCE@ 33 @RELEASED_SINCE@
34 #for search_term in $filters.search: 34 #for search_term in $filters.search:
35 --search '$filters.search_term' 35 --search '$filters.search_term'
36 #end for 36 #end for
37 #if $uncompressed 37 #if $uncompressed
38 && unzip ncbi_dataset.zip 38 && 7z x -y ncbi_dataset.zip
39 #else 39 #else
40 && unzip -l ncbi_dataset.zip > ncbi_dataset.txt 40 && 7z l ncbi_dataset.zip > ncbi_dataset.txt
41 #end if 41 #end if
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <section name="query" title="Query" expanded="true"> 44 <section name="query" title="Query" expanded="true">
45 <conditional name="subcommand"> 45 <conditional name="subcommand">
231 <param name="exclude_genomic_cds" value="true"/> 231 <param name="exclude_genomic_cds" value="true"/>
232 <param name="exclude_gff3" value="true"/> 232 <param name="exclude_gff3" value="true"/>
233 <param name="uncompressed" value="true"/> 233 <param name="uncompressed" value="true"/>
234 <param name="released_before" value="01/02/2007"></param> 234 <param name="released_before" value="01/02/2007"></param>
235 <output_collection name="sequence_report"> 235 <output_collection name="sequence_report">
236 <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/> 236 <element name="GCF_000001405.40">
237 <assert_contents>
238 <has_text text="assignedMoleculeLocationType"/>
239 </assert_contents>
240 </element>
237 </output_collection> 241 </output_collection>
238 </test> 242 </test>
239 <test expect_num_outputs="5"> 243 <test expect_num_outputs="5">
240 <conditional name="query|subcommand"> 244 <conditional name="query|subcommand">
241 <param name="download_by" value="accession"></param> 245 <param name="download_by" value="accession"></param>
253 <output_collection name="genome_fasta" type="list:list" count="1"> 257 <output_collection name="genome_fasta" type="list:list" count="1">
254 <element name="GCF_000146045.2"> 258 <element name="GCF_000146045.2">
255 <element name="chrI"> 259 <element name="chrI">
256 <assert_contents> 260 <assert_contents>
257 <has_text text=">NC_001133.9"/> 261 <has_text text=">NC_001133.9"/>
262 </assert_contents>
263 </element>
264 </element>
265 </output_collection>
266 </test>
267 <test expect_num_outputs="3">
268 <conditional name="query|subcommand">
269 <param name="download_by" value="accession"></param>
270 <conditional name="text_or_file">
271 <param name="text_or_file" value="text"></param>
272 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"></param>
273 </conditional>
274 </conditional>
275 <param name="exclude_protein" value="true"/>
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"/>
281 <output_collection name="genome_fasta" type="list:list" count="2">
282 <element name="GCF_000146045.2">
283 <element name="chrI">
284 <assert_contents>
285 <has_text text=">NC_001133.9"/>
286 </assert_contents>
287 </element>
288 </element>
289 <element name="GCF_000002945.1">
290 <element name="chrI">
291 <assert_contents>
292 <has_text text=">NC_003424.3"/>
258 </assert_contents> 293 </assert_contents>
259 </element> 294 </element>
260 </element> 295 </element>
261 </output_collection> 296 </output_collection>
262 </test> 297 </test>