Mercurial > repos > iuc > ncbi_datasets

annotate datasets_genome.xml @ 3:d19bb3e590b6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 666290ba9b99eec10ab3da91d9bef816af4a1fb9"
author iuc
date Mon, 28 Feb 2022 11:10:11 +0000
parents 1a7773882d2c
children 6c829a430475
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1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE" version="@TOOL_VERSION@">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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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[
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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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 $query.subcommand.text_or_file.accession.split(' ') if x)
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13 #else
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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14 --inputfile '$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
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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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">
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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"
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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
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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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
91 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list">
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
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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
93 <filter>uncompressed and file_choices['exclude_seq']</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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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
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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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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97 <filter>uncompressed and file_choices['exclude_genomic_cds']</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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98 </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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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
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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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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101 <filter>uncompressed and file_choices['exclude_gff3']</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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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
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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
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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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
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105 <filter>uncompressed and file_choices['exclude_rna']</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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106 </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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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:
diff changeset
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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
109 <filter>uncompressed and file_choices['exclude_protein']</filter>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
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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
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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
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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>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
128 <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
129 <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
130 <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
131 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
132 <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
133 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
134 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
135 </test>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
136 <test expect_num_outputs="5">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
137 <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
138 <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
139 <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
140 <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
141 <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:
diff changeset
142 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
143 </conditional>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
144 <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
145 <param name="released_before" value="01/01/2007"></param>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
146 <param name="exclude_genomic_cds" value="true"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
147 <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:
diff changeset
148 <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
149 <assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
150 <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:
diff changeset
151 </assert_contents>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
152 </output>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
153 <output_collection name="sequence_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
154 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
155 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
156 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
157 <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
158 <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
159 <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:
diff changeset
160 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
161 <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
162 <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
163 <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:
diff changeset
164 </output_collection>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
165 </test>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
iuc
parents:
diff changeset
166 <test expect_num_outputs="4">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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167 <conditional name="query|subcommand">
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168 <param name="download_by" value="accession"></param>
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169 <conditional name="text_or_file">
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170 <param name="text_or_file" value="file"></param>
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171 <param name="inputfile" value="accessions.txt"></param>
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172 </conditional>
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173 </conditional>
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174 <param name="include_gbff" value="true"/>
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175 <param name="exclude_seq" value="false"/>
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176 <param name="exclude_gff3" value="true"/>
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177 <param name="uncompressed" value="true"/>
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178 <param name="released_before" value="01/02/2007"></param>
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179 <output name="genome_data_report">
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180 <assert_contents>
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181 <has_text text="SAMN02604181"/>
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182 </assert_contents>
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183 </output>
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184 <output_collection name="sequence_report" type="list">
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185 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.seq.rpt.jsonl" compare="contains"/>
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186 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.seq.rpt.jsonl" compare="contains"/>
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187 </output_collection>
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188 <output_collection name="genomic_gff" type="list">
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189 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
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190 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
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191 </output_collection>
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192 <output_collection name="genomic_gbff" type="list">
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193 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
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194 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
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195 </output_collection>
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196 </test>
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197 </tests>
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198 <help>
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199 <![CDATA[
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200 **Download Genome Datasets from NCBI**
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201
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202 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
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203 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
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204
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205 Tthe default genome dataset includes the following files (if available):
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206 * genomic.fna (genomic sequences)
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207 * rna.fna (transcript sequences)
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208 * protein.faa (protein sequences)
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209 * genomic.gff (genome annotation in gff3 format)
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210 * data_report.jsonl (data report with genome assembly and annotation metadata)
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211 * dataset_catalog.json (a list of files and file types included in the dataset)
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212 ]]>
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213 </help>
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214
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215 </tool>