annotate datasets_genome.xml @ 6:5a2656cc84cb draft

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
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6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
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1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@">
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2 <description>download genome sequence, annotation and metadata</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"></expand>
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7 <command><![CDATA[
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8 @SETUP_CERTIFICATES@
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9 datasets download genome $query.subcommand.download_by
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10 #if $query.subcommand.download_by == 'accession':
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11 #if $query.subcommand.text_or_file.text_or_file == 'text':
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12 #echo " ".join(f"'{x}'" for x in $query.subcommand.text_or_file.accession.split(' ') if x)
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13 #else
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14 --inputfile '$query.subcommand.text_or_file.inputfile'
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15 #end if
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16 #else:
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17 '$query.subcommand.taxon'
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18 #end if
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19 $filters.reference
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20 $filters.annotated
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21 #if $filters.assembly_level:
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22 --assembly-level $filters.assembly_level
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23 #end if
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24 #if $filters.assembly_source:
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25 --assembly-source $filters.assembly_source
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26 #end if
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27 #if $filters.chromosomes:
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28 --chromosomes '$filters.chromosomes'
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29 #end if
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30 @EXCLUDES_GENOME@
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31 @INCLUDES_GENOME@
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32 @RELEASED_BEFORE@
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33 @RELEASED_SINCE@
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34 #for search_term in $filters.search:
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35 --search '$filters.search_term'
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36 #end for
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37 #if $uncompressed
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38 && unzip ncbi_dataset.zip
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39 #else
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40 && unzip -l ncbi_dataset.zip > ncbi_dataset.txt
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41 #end if
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42 ]]></command>
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43 <inputs>
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44 <section name="query" title="Query" expanded="true">
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45 <conditional name="subcommand">
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46 <param name="download_by" type="select" label="Choose how to find genomes to download">
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47 <option value="accession">Download by NCBI assembly or BioProject accession</option>
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48 <option value="taxon">Download by taxon</option>
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49 </param>
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50 <when value="accession">
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51 <expand macro="text_or_file"/>
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52 </when>
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53 <when value="taxon">
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54 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."></param>
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55 </when>
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56 </conditional>
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57 </section>
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58 <section name="filters" title="Filters and Limit">
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59 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
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60 <expand macro="annotation"></expand>
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61 <expand macro="assembly_level"></expand>
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62 <expand macro="assembly_source"></expand>
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63 <expand macro="chromosomes"></expand>
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64 <expand macro="released_options"></expand>
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65 <expand macro="released_options" before_or_after="since"></expand>
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66
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67 <repeat name="search" title="Add search terms">
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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"/>
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69 </repeat>
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70 </section>
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71 <section name="file_choices" title="File Choices" expanded="true">
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72 <expand macro="excludes_genome"></expand>
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73 <expand macro="includes_genome"></expand>
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74 </section>
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75 <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/>
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76 </inputs>
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77 <outputs>
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78 <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip">
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79 <filter>not uncompressed</filter>
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80 </data>
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81 <data name="archive_contents" format="txt" label="Archive Contents" from_work_dir="ncbi_dataset.txt">
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82 <filter>not uncompressed</filter>
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83 </data>
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84 <data name="genome_data_report" format="json" label="NCBI Genome Datasets: Data Report" from_work_dir="ncbi_dataset/data/assembly_data_report.jsonl">
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85 <filter>uncompressed</filter>
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86 </data>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
87 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
89 <filter>uncompressed</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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90 </collection>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
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>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
93 <filter>uncompressed and not file_choices['exclude_seq']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
94 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
95 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
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>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
97 <filter>uncompressed and not file_choices['exclude_genomic_cds']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
98 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
99 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
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>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
101 <filter>uncompressed and not file_choices['exclude_gff3']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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102 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
103 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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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>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
105 <filter>uncompressed and not file_choices['exclude_rna']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
106 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
107 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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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>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
109 <filter>uncompressed and not file_choices['exclude_protein']</filter>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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110 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
111 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
113 <filter>uncompressed and file_choices['include_gbff']</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
114 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
115 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
117 <filter>uncompressed and file_choices['include_gtf']</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
118 </collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
119 </outputs>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
120 <tests>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
121 <test expect_num_outputs="2">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
122 <conditional name="query|subcommand">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
123 <param name="download_by" value="taxon"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
124 <param name="text_or_file" value="text"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
125 <param name="taxon" value="human"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
126 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
127 <param name="chromosomes" value="21"></param>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
128 <param name="exclude_protein" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
129 <param name="exclude_rna" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
130 <param name="exclude_seq" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
131 <param name="exclude_genomic_cds" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
132 <param name="exclude_gff3" value="true"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
133 <param name="uncompressed" value="false"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
134 <param name="released_before" value="01/01/2018"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
135 <output name="archive_contents">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
136 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
137 <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
138 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
139 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
140 </test>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
141 <test expect_num_outputs="2">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
142 <conditional name="query|subcommand">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
143 <param name="download_by" value="taxon"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
144 <param name="text_or_file" value="text"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
145 <param name="taxon" value="human"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
146 </conditional>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
147 <param name="chromosomes" value="21"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
148 <param name="uncompressed" value="false"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
149 <param name="exclude_protein" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
150 <param name="exclude_rna" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
151 <param name="exclude_seq" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
152 <param name="exclude_genomic_cds" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
153 <param name="exclude_gff3" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
154 <param name="assembly_level" value="chromosome"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
155 <param name="released_before" value="01/01/2018"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
156 <output name="archive_contents">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
157 <assert_contents>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
158 <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
159 </assert_contents>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
160 </output>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
161 </test>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
162 <test expect_num_outputs="4">
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
163 <conditional name="query|subcommand">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
164 <param name="download_by" value="accession"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
165 <conditional name="text_or_file">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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166 <param name="text_or_file" value="text"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
167 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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168 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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169 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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170 <param name="uncompressed" value="true"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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171 <param name="released_before" value="01/01/2007"></param>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
172 <param name="exclude_protein" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
173 <param name="exclude_rna" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
174 <param name="exclude_seq" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
175 <param name="exclude_gff3" value="true"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
176 <param name="include_gtf" value="true"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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177 <output name="genome_data_report">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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178 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
179 <has_text text="GCF_000013305.1"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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180 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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181 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
182 <output_collection name="genomic_gtf" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
183 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
184 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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185 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
186 <output_collection name="genomic_cds" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
187 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
188 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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189 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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190 </test>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
191 <test expect_num_outputs="4">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
192 <conditional name="query|subcommand">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
193 <param name="download_by" value="accession"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
194 <conditional name="text_or_file">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
195 <param name="text_or_file" value="file"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
196 <param name="inputfile" value="accessions.txt"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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197 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
198 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
199 <param name="include_gbff" value="true"/>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
200 <param name="exclude_protein" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
201 <param name="exclude_rna" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
202 <param name="exclude_seq" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
203 <param name="exclude_genomic_cds" value="true"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
204 <param name="uncompressed" value="true"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
205 <param name="released_before" value="01/02/2007"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
206 <output name="genome_data_report">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
207 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
208 <has_text text="SAMN02604181"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
209 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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diff changeset
210 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
211 <output_collection name="genomic_gff" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
212 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
213 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
214 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
215 <output_collection name="genomic_gbff" type="list">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
216 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
217 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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218 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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219 </test>
5
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
220 <test expect_num_outputs="2">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
221 <conditional name="query|subcommand">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
222 <param name="download_by" value="accession"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
223 <conditional name="text_or_file">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
224 <param name="text_or_file" value="text"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
225 <param name="accession" value="GCF_000001405.40"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
226 </conditional>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
227 </conditional>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
228 <param name="exclude_protein" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
229 <param name="exclude_rna" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
230 <param name="exclude_seq" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
231 <param name="exclude_genomic_cds" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
232 <param name="exclude_gff3" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
233 <param name="uncompressed" value="true"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
234 <param name="released_before" value="01/02/2007"></param>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
235 <output_collection name="sequence_report">
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
236 <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
6c829a430475 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit a58a3198ea1b60b6aa9567c6c65f00f8361794f6"
iuc
parents: 0
diff changeset
237 </output_collection>
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iuc
parents: 0
diff changeset
238 </test>
6
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
239 <test expect_num_outputs="3">
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iuc
parents: 5
diff changeset
240 <conditional name="query|subcommand">
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iuc
parents: 5
diff changeset
241 <param name="download_by" value="accession"></param>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
242 <conditional name="text_or_file">
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
243 <param name="text_or_file" value="text"></param>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
244 <param name="accession" value="GCF_000146045.2"></param>
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iuc
parents: 5
diff changeset
245 </conditional>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
246 </conditional>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
247 <param name="exclude_protein" value="true"/>
5a2656cc84cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
iuc
parents: 5
diff changeset
248 <param name="exclude_rna" value="true"/>
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iuc
parents: 5
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249 <param name="exclude_seq" value="false"/>
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250 <param name="exclude_genomic_cds" value="true"/>
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251 <param name="exclude_gff3" value="true"/>
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252 <param name="uncompressed" value="true"/>
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253 <output_collection name="genome_fasta" type="list:list" count="1">
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254 <element name="GCF_000146045.2">
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255 <element name="chrI">
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256 <assert_contents>
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257 <has_text text=">NC_001133.9"/>
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258 </assert_contents>
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259 </element>
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260 </element>
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261 </output_collection>
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262 </test>
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263 </tests>
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264 <help>
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265 <![CDATA[
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266 **Download Genome Datasets from NCBI**
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267
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268 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
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269 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
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270
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271 Tthe default genome dataset includes the following files (if available):
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272 * data_report.jsonl (genome assembly and annotation metadata, not always available)
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273 * genomic.fna (genomic sequences)
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274 * rna.fna (transcript sequences)
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275 * protein.faa (protein sequences)
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276 * genomic.gff (genome annotation in gff3 format)
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277 * dataset_catalog.json (a list of files and file types included in the dataset)
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278 ]]>
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279 </help>
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280
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281 </tool>