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comparison datasets_genome.xml @ 6:5a2656cc84cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
author iuc
date Mon, 06 Jun 2022 13:41:05 +0000
parents 6c829a430475
children 0622d99c2619
comparison
equal deleted inserted replaced
5:6c829a430475 6:5a2656cc84cb
1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE" version="@TOOL_VERSION@"> 1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@">
2 <description>download genome sequence, annotation and metadata</description> 2 <description>download genome sequence, annotation and metadata</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"></expand>
86 </data> 86 </data>
87 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list"> 87 <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> 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>
89 <filter>uncompressed</filter> 89 <filter>uncompressed</filter>
90 </collection> 90 </collection>
91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list"> 91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
92 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/.*(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets> 92 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/(?P&lt;identifier_1&gt;.*?)\.(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
93 <filter>uncompressed and not file_choices['exclude_seq']</filter> 93 <filter>uncompressed and not file_choices['exclude_seq']</filter>
94 </collection> 94 </collection>
95 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list"> 95 <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> 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>
97 <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter> 97 <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter>
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" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
237 </output_collection>
238 </test>
239 <test expect_num_outputs="3">
240 <conditional name="query|subcommand">
241 <param name="download_by" value="accession"></param>
242 <conditional name="text_or_file">
243 <param name="text_or_file" value="text"></param>
244 <param name="accession" value="GCF_000146045.2"></param>
245 </conditional>
246 </conditional>
247 <param name="exclude_protein" value="true"/>
248 <param name="exclude_rna" value="true"/>
249 <param name="exclude_seq" value="false"/>
250 <param name="exclude_genomic_cds" value="true"/>
251 <param name="exclude_gff3" value="true"/>
252 <param name="uncompressed" value="true"/>
253 <output_collection name="genome_fasta" type="list:list" count="1">
254 <element name="GCF_000146045.2">
255 <element name="chrI">
256 <assert_contents>
257 <has_text text=">NC_001133.9"/>
258 </assert_contents>
259 </element>
260 </element>
237 </output_collection> 261 </output_collection>
238 </test> 262 </test>
239 </tests> 263 </tests>
240 <help> 264 <help>
241 <![CDATA[ 265 <![CDATA[