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comparison datasets_genome.xml @ 7:0622d99c2619 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210
author iuc
date Tue, 07 Jun 2022 17:39:19 +0000
parents 5a2656cc84cb
children b2ae7186d41f
comparison
equal deleted inserted replaced
6:5a2656cc84cb 7:0622d99c2619
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@+galaxy@VERSION_SUFFIX@">
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>
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:list"> 91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
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> 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>
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>
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> 237 </output_collection>
238 </test> 238 </test>
239 <test expect_num_outputs="3"> 239 <test expect_num_outputs="5">
240 <conditional name="query|subcommand"> 240 <conditional name="query|subcommand">
241 <param name="download_by" value="accession"></param> 241 <param name="download_by" value="accession"></param>
242 <conditional name="text_or_file"> 242 <conditional name="text_or_file">
243 <param name="text_or_file" value="text"></param> 243 <param name="text_or_file" value="text"></param>
244 <param name="accession" value="GCF_000146045.2"></param> 244 <param name="accession" value="GCF_000146045.2"></param>
245 </conditional> 245 </conditional>
246 </conditional> 246 </conditional>
247 <param name="exclude_protein" value="true"/> 247 <param name="exclude_protein" value="true"/>
248 <param name="exclude_rna" value="true"/> 248 <param name="exclude_rna" value="false"/>
249 <param name="exclude_seq" value="false"/> 249 <param name="exclude_seq" value="false"/>
250 <param name="exclude_genomic_cds" value="true"/> 250 <param name="exclude_genomic_cds" value="false"/>
251 <param name="exclude_gff3" value="true"/> 251 <param name="exclude_gff3" value="true"/>
252 <param name="uncompressed" value="true"/> 252 <param name="uncompressed" value="true"/>
253 <output_collection name="genome_fasta" type="list:list" count="1"> 253 <output_collection name="genome_fasta" type="list:list" count="1">
254 <element name="GCF_000146045.2"> 254 <element name="GCF_000146045.2">
255 <element name="chrI"> 255 <element name="chrI">