Mercurial > repos > iuc > ncbi_datasets

annotate datasets_genome.xml @ 20:35d32c807c23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb
author iuc
date Fri, 26 Dec 2025 17:16:51 +0000
parents 9a10a6449901
children
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1 <tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <stdio>
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10 <regex match="Warning" source="stderr" level="warning" description=""/>
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11 <regex match="skipping" source="stderr" level="warning" description=""/>
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12 <regex match="ERROR" level="fatal"/>
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #import re
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16 @SETUP_CERTIFICATES@
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17 datasets download genome $query.subcommand.download_by
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18 #if $query.subcommand.download_by == 'accession':
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19 #if $query.subcommand.text_or_file.text_or_file == 'text':
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20 #echo " ".join(f"'{x}'" for x in re.split(" |,", str($query.subcommand.text_or_file.accession)) if x)
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21 #else
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22 --inputfile '$query.subcommand.text_or_file.inputfile'
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23 #end if
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24 #else:
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25 '$query.subcommand.taxon_positional'
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26 $query.subcommand.tax_exact_match
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27 #end if
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28 $filters.reference
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29 $filters.annotated
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30 #if $filters.assembly_level:
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31 --assembly-level $filters.assembly_level
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32 #end if
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33 --assembly-version $filters.assembly_version
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34 #if $filters.assembly_source:
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35 --assembly-source $filters.assembly_source
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36 #end if
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37 #if $filters.chromosomes:
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38 --chromosomes '$filters.chromosomes'
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39 #end if
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40 $filters.exclude_atypical
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41 #if $filters.mag:
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42 --mag '$filters.mag'
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43 #end if
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44
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45 @INCLUDE@
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46 @RELEASED_BEFORE@
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47 @RELEASED_AFTER@
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48 #for search_term in $filters.search:
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49 --search '$search_term.search'
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50 #end for
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51 --no-progressbar
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52 --dehydrated
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54 ## produce TSV report file
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55 && dataformat tsv genome
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56 --package ncbi_dataset.zip
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57 --fields #echo ",".join($file_choices.report_columns)
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58 > genome_data_report.tsv
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60 ## unzip and rehydrate if any data is to be downloaded (include is not None)
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61 #if $file_choices.include
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62 ## unzip
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63 && unzip ncbi_dataset.zip
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65 ## rehydrate
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66 && datasets rehydrate
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67 --directory ./
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68 #if not $file_choices.decompress
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69 --gzip
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70 #end if
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71 --max-workers \${NCBI_DATASETS_MAX_WORKERS:-10}
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73 ## rename all faa, fna (resp faa.gz, fna.gz) to fasta (resp fasta.gz) to allow discovery
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74 && find ncbi_dataset \( -name "*.faa" -o -name "*.fna" -o -name "*.faa.gz" -o -name "*.fna.gz" \) -exec sh -c 'mv {} \$(echo {} | sed "s/.f[an]a\(.gz\)\?\$/.fasta\1/")' \;
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75
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76 ## unzip all compressed (non-fasta) files (jsonl files are just named .gz)
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77 ## note "not decompress" means that the datasets are provided uncompressed (datasets rehydrate is called we --gzip)
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78 ## in this case we need to decompress all datasets that don't have a Galaxy datatype allowing for compression
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79 && find ncbi_dataset -name "*.jsonl.gz" -exec sh -c 'mv {} \$(dirname {})/\$(basename {} .gz)' \;
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80 #if not $file_choices.decompress
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81 && find ncbi_dataset \( -name "*.gz" ! -name "*fasta.gz" \) -exec gunzip {} \;
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82 #end if
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84 #if "seq-report" in $file_choices.include
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85 && find ncbi_dataset -name sequence_report.jsonl -exec sh -c 'dataformat tsv genome-seq --inputfile {} > \$(dirname {})/\$(basename {} .jsonl).tsv' \;
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86 #end if
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87
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88 && true ## because Galaxy removes trailing ; from command
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89 #end if
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90 ]]></command>
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91 <inputs>
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92 <section name="query" title="Query" expanded="true">
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93 <conditional name="subcommand">
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94 <param name="download_by" type="select" label="Choose how to find genomes to download">
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95 <option value="accession">By NCBI assembly or BioProject accession</option>
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96 <option value="taxon">By taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)</option>
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97 </param>
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98 <when value="accession">
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99 <expand macro="text_or_file"/>
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100 </when>
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101 <when value="taxon">
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102 <expand macro="taxon_positional"/>
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103 <param argument="--tax-exact-match" type="boolean" truevalue="--tax-exact-match" falsevalue="" label="Exclude sub-species when a species-level taxon is specified"/>
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104 </when>
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105 </conditional>
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106 </section>
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107 <section name="filters" title="Filters and Limit">
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108 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
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109 <expand macro="annotation"/>
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110 <expand macro="assembly_level"/>
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111 <param argument="--assembly-version" type="select" label="Assembly version(s)">
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112 <option value="latest">Latest</option>
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113 <option value="all">All</option>
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114 </param>
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115 <expand macro="assembly_source"/>
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116 <expand macro="chromosomes"/>
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117 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/>
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118 <param argument="--mag" type="select" multiple="false" optional="true" label="Filter metagenome assembled genomes (MAGs)">
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119 <option value="only" selected="false">Limit to MAGs</option>
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120 <option value="exclude" selected="false">Exclude MAGs</option>
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121 </param>
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122 <expand macro="released_options"/>
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123 <expand macro="released_options" before_or_after="after"/>
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124 <repeat name="search" title="Add search terms">
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125 <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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126 </repeat>
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127 </section>
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128 <section name="file_choices" title="Output options" expanded="true">
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129 <expand macro="tsv_report_columns">
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130 <option value="accession" selected="true">accession</option>
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131 <option value="organism-name" selected="true">organism-name</option>
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132 <option value="assminfo-submitter" selected="true">assminfo-submitter</option>
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133 <option value="assminfo-name" selected="true">assminfo-name</option>
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134 </expand>
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135 <expand macro="include">
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136 <expand macro="genome_includes"/>
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137 </expand>
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138 <param name="decompress" type="boolean" label="Decompress FASTA" help="By default FASTA files are provided zipped (fasta.gz) if this is checked the data will be decompressed"/>
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139 </section>
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140 </inputs>
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141 <outputs>
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142 <data name="genome_data_report" format="tabular" label="NCBI Genome Datasets: Data Report" from_work_dir="genome_data_report.tsv"/>
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143 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
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144 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.tsv" ext="tabular" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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145 <filter>file_choices['include'] and "seq-report" in file_choices['include']</filter>
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146 </collection>
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147 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
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148 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?\.(?P&lt;ext&gt;fasta(\.gz)?)" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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149 <filter>file_choices['include'] and "genome" in file_choices['include']</filter>
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150 </collection>
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151 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
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152 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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153 <filter>file_choices['include'] and "rna" in file_choices['include']</filter>
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154 </collection>
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155 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
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156 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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157 <filter>file_choices['include'] and "protein" in file_choices['include']</filter>
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158 </collection>
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159 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
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160 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.(?P&lt;ext&gt;fasta(\.gz)?)$" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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161 <filter>file_choices['include'] and "cds" in file_choices['include']</filter>
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162 </collection>
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163 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
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164 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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165 <filter>file_choices['include'] and "gff3" in file_choices['include']</filter>
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166 </collection>
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167 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
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168 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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169 <filter>file_choices['include'] and "gtf" in file_choices['include']</filter>
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170 </collection>
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171 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
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172 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="txt" directory="ncbi_dataset/data/" recurse="true" match_relative_path="true"/>
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173 <filter>file_choices['include'] and "gbff" in file_choices['include']</filter>
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174 </collection>
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175 </outputs>
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176 <tests>
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177 <test expect_num_outputs="3">
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178 <conditional name="query|subcommand">
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179 <param name="download_by" value="taxon"/>
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180 <param name="taxon_positional" value="human"/>
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181 </conditional>
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182 <section name="filters">
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183 <param name="chromosomes" value="21"/>
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184 <param name="released_before" value="01/01/2018"/>
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185 </section>
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186 <section name="file_choices">
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187 <!-- include a sequence (which should be downloaded as fasta.gz)
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188 and one non-sequence (which should be decompressed) output -->
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189 <param name="include" value="rna,gff3"/>
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190 </section>
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191 <output name="genome_data_report">
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192 <assert_contents>
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193 <has_text text="Assembly Accession&#9;Assembly Name&#9;Assembly Submitter&#9;Organism Name"/>
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194 <has_n_lines min="140"/>
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195 <has_n_columns n="4"/>
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196 </assert_contents>
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197 </output>
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198 <output_collection name="rna_fasta" type="list">
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199 <element name="GCF_000306695.2" decompress="true">
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200 <assert_contents>
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201 <has_text text="&gt;"/>
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202 </assert_contents>
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203 </element>
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204 </output_collection>
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205 <output_collection name="genomic_gff" type="list">
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206 <element name="GCF_000306695.2">
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207 <assert_contents>
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208 <has_n_lines min="1000000"/>
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209 <has_line line="##gff-version 3"/>
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210 <has_n_columns n="9" comment="#"/>
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211 </assert_contents>
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212 </element>
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213 </output_collection>
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214 <assert_command>
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215 <has_text text="gunzip"/>
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216 </assert_command>
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217 </test>
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218 <test expect_num_outputs="2">
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219 <conditional name="query|subcommand">
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220 <param name="download_by" value="taxon"/>
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221 <param name="taxon_positional" value="Norway rat"/>
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222 </conditional>
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223 <section name="filters">
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224 <param name="chromosomes" value="MT"/>
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225 </section>
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226 <section name="file_choices">
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227 <param name="include" value="genome"/>
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228 <param name="decompress" value="true"/>
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229 </section>
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230 <output_collection name="genome_fasta" type="list:list" count="9">
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231 <expand macro="genome_fasta_assert" el1="GCA_000001895.4" el2="chrMT" expression="&gt;"/>
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232 <expand macro="genome_fasta_assert" el1="GCA_015227675.2" el2="chrMT" expression="&gt;"/>
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233 <expand macro="genome_fasta_assert" el1="GCA_036323735.1" el2="chrMT" expression="&gt;"/>
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234 <expand macro="genome_fasta_assert" el1="GCA_041222355.1" el2="chrMT" expression="&gt;"/>
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235 <expand macro="genome_fasta_assert" el1="GCA_045687965.1" el2="chrMT" expression="&gt;"/>
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236 <expand macro="genome_fasta_assert" el1="GCA_045687995.1" el2="chrMT" expression="&gt;"/>
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237 <expand macro="genome_fasta_assert" el1="GCA_045688005.1" el2="chrMT" expression="&gt;"/>
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238 <expand macro="genome_fasta_assert" el1="GCF_000001895.5" el2="chrMT" expression="&gt;"/>
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239 <expand macro="genome_fasta_assert" el1="GCF_015227675.2" el2="chrMT" expression="&gt;"/>
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240 <!-- According to https://github.com/ncbi/datasets/issues/188, the following should not be included among the returned results anymore 09/2023 -->
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241 <!--
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242 <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/>
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243 <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/>
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244 -->
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245 </output_collection>
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246 <output name="genome_data_report">
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247 <assert_contents>
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248 <has_text text="Rattus norvegicus"/>
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249 <has_n_columns n="4"/>
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250 </assert_contents>
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251 </output>
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252 </test>
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253 <!-- same as previous test but assembly_source=refseq, which removes all of the genomes -->
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254 <test expect_failure="true">
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255 <conditional name="query|subcommand">
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256 <param name="download_by" value="taxon"/>
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257 <param name="taxon_positional" value="human"/>
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258 </conditional>
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259 <section name="filters">
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260 <param name="chromosomes" value="21"/>
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261 <param name="assembly_level" value="chromosome,complete"/>
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262 <param name="assembly_source" value="refseq"/>
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263 <param name="released_before" value="01/01/2018"/>
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264 </section>
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265 <section name="file_choices">
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266 <param name="include" value="genome"/>
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267 <param name="decompress" value="true"/>
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268 </section>
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269 <assert_stderr>
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270 <has_text text="no genome assemblies were found"/>
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271 </assert_stderr>
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272 <!-- In the current state of the NCBI tool/DB, no output to check.
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273 But the returned results seem to change from time to time and it might
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274 be necessary to re-enable this code block if the test fails in the future. -->
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275 <!--
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276 <output_collection name="genome_fasta" type="list:list" count="2">
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277 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
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278 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
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279 </output_collection>
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280 <output name="genome_data_report">
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281 <assert_contents>
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282 <has_text text="Homo sapiens"/>
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283 <has_n_lines n="5"/>
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284 <has_n_columns n="4"/>
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285 </assert_contents>
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286 </output> -->
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287 </test>
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288 <test expect_num_outputs="4">
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289 <conditional name="query|subcommand">
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290 <param name="download_by" value="accession"/>
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291 <conditional name="text_or_file">
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292 <param name="text_or_file" value="text"/>
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293 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"/>
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294 </conditional>
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295 </conditional>
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296 <section name="filters">
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297 <param name="released_before" value="01/01/2007"/>
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298 </section>
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299 <section name="file_choices">
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300 <param name="include" value="seq-report,gtf,cds"/>
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301 <param name="decompress" value="true"/>
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302 </section>
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303 <output name="genome_data_report">
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304 <assert_contents>
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305 <has_text text="GCF_000013305.1"/>
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306 <has_n_lines n="3"/>
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307 <has_n_columns n="4"/>
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308 </assert_contents>
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309 </output>
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310 <output_collection name="sequence_report" type="list" count="2">
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311 <element name="GCF_000007445.1">
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312 <assert_contents>
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313 <has_text text="GCF_000007445.1"/>
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314 <has_n_lines n="2"/>
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315 <has_n_columns n="15"/>
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316 </assert_contents>
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317 </element>
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318 <element name="GCF_000013305.1">
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319 <assert_contents>
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320 <has_text text="GCF_000013305.1"/>
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321 <has_n_lines n="2"/>
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322 <has_n_columns n="15"/>
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323 </assert_contents>
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324 </element>
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325 </output_collection>
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326 <output_collection name="genomic_gtf" type="list" count="2">
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327 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
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328 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
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329 </output_collection>
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330 <output_collection name="genomic_cds" type="list">
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331 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/>
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332 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
0
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333 </output_collection>
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334 </test>
3
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335 <test expect_num_outputs="4">
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336 <conditional name="query|subcommand">
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337 <param name="download_by" value="accession"/>
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338 <conditional name="text_or_file">
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339 <param name="text_or_file" value="file"/>
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340 <param name="inputfile" value="accessions.txt"/>
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341 </conditional>
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342 </conditional>
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343 <section name="filters">
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344 <param name="released_before" value="01/01/2007"/>
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345 </section>
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346 <section name="file_choices">
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347 <param name="include" value="seq-report,gff3,gbff"/>
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348 <param name="decompress" value="true"/>
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349 </section>
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350 <output name="genome_data_report">
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351 <assert_contents>
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352 <has_text text="GCF_000013305.1"/>
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353 <has_text text="GCF_000007445.1"/>
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354 <has_n_lines n="3"/>
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355 <has_n_columns n="4"/>
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356 </assert_contents>
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357 </output>
0
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358 <output_collection name="genomic_gff" type="list">
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359 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
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360 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
0
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361 </output_collection>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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362 <output_collection name="genomic_gbff" type="list">
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363 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
3
c87df3f9e19d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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364 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
0
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365 </output_collection>
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366 </test>
14
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367 <!-- should not fail https://github.com/ncbi/datasets/issues/194 -->
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368 <test expect_num_outputs="2">
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369 <conditional name="query|subcommand">
13
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370 <param name="download_by" value="accession"/>
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parents: 3
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371 <conditional name="text_or_file">
13
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372 <param name="text_or_file" value="text"/>
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373 <param name="accession" value="GCF_000001405"/>
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374 </conditional>
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375 </conditional>
20
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diff changeset
376 <section name="filters">
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377 <param name="released_before" value="01/01/2015"/>
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diff changeset
378 <param name="assembly_version" value="all"/>
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379 </section>
14
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380 <section name="file_choices">
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diff changeset
381 <param name="include" value="seq-report"/>
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382 </section>
16
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diff changeset
383 <output name="genome_data_report">
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diff changeset
384 <!-- assert that we get at least the 16 versions available at the time of writing this test -->
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385 <assert_contents>
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diff changeset
386 <has_text text="GCF_000001405" min="16"/>
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diff changeset
387 <has_n_lines min="16"/>
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388 <has_n_columns n="4"/>
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389 </assert_contents>
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diff changeset
390 </output>
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parents: 15
diff changeset
391 <!--not testing the collection output. the count will change over time
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diff changeset
392 and this can't be tested for at the moment
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393 <output_collection name="sequence_report" type="list" count="16"/> -->
8
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394 </test>
10
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diff changeset
395 <test expect_num_outputs="5">
9
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396 <conditional name="query|subcommand">
13
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397 <param name="download_by" value="accession"/>
9
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398 <conditional name="text_or_file">
13
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diff changeset
399 <param name="text_or_file" value="text"/>
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400 <param name="accession" value="GCF_000146045.2"/>
9
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401 </conditional>
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402 </conditional>
14
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403 <section name="file_choices">
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diff changeset
404 <param name="include" value="genome,protein,rna,cds"/>
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diff changeset
405 <param name="decompress" value="true"/>
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406 </section>
9
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diff changeset
407 <output_collection name="genome_fasta" type="list:list" count="1">
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diff changeset
408 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression="&gt;NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
9
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diff changeset
409 </output_collection>
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diff changeset
410 <output_collection name="protein_fasta" type="list" count="1">
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diff changeset
411 <element name="GCF_000146045.2" decompress="true">
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412 <assert_contents>
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413 <has_text text="&gt;"/>
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414 </assert_contents>
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415 </element>
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416 </output_collection>
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417 <output_collection name="rna_fasta" type="list" count="1">
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418 <element name="GCF_000146045.2" decompress="true">
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419 <assert_contents>
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420 <has_text text="&gt;"/>
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421 </assert_contents>
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422 </element>
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423 </output_collection>
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424 </test>
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425 <!-- same as the previous test, but use the default value for decompress,
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426 see comment at the beginning of the tests -->
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427 <test expect_num_outputs="5">
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428 <conditional name="query|subcommand">
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429 <param name="download_by" value="accession"/>
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430 <conditional name="text_or_file">
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431 <param name="text_or_file" value="text"/>
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432 <param name="accession" value="GCF_000146045.2"/>
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433 </conditional>
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434 </conditional>
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435 <section name="file_choices">
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436 <param name="include" value="genome,protein,rna,cds"/>
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437 </section>
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438 <output_collection name="genome_fasta" type="list:list" count="1">
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439 <element name="GCF_000146045.2">
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440 <element name="GCF_000146045.2_R64" ftype="fasta.gz">
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441 <assert_contents>
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442 <has_size value="3843460" delta="2000"/>
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443 </assert_contents>
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444 </element>
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445 </element>
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446 </output_collection>
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447 <output_collection name="protein_fasta" type="list" count="1">
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448 <element name="GCF_000146045.2" ftype="fasta.gz">
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449 <assert_contents>
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450 <has_size value="1847862" delta="2000"/>
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451 </assert_contents>
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452 </element>
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453 </output_collection>
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454 <output_collection name="rna_fasta" type="list" count="1">
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455 <element name="GCF_000146045.2" ftype="fasta.gz">
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456 <assert_contents>
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457 <has_size min="2700000" max="2800000"/>
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458 </assert_contents>
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459 </element>
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460 </output_collection>
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461 </test>
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462 <test expect_num_outputs="3">
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463 <conditional name="query|subcommand">
13
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464 <param name="download_by" value="accession"/>
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465 <conditional name="text_or_file">
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466 <param name="text_or_file" value="text"/>
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467 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"/>
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468 </conditional>
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469 </conditional>
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470 <section name="file_choices">
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471 <param name="include" value="seq-report,genome"/>
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472 <param name="decompress" value="true"/>
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473 </section>
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474 <output_collection name="sequence_report" type="list" count="2"/>
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475 <output_collection name="genome_fasta" type="list:list" count="2">
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476 <expand macro="genome_fasta_assert" el1="GCF_000002945.2" el2="GCF_000002945.2_ASM294v3" expression="&gt;NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe.*" expression_n="4"/>
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477 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression="&gt;NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc].*" expression_n="17"/>
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478 </output_collection>
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479 </test>
16
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480 <!-- tax_exact_match should filter out strains
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481 https://github.com/ncbi/datasets/issues/187 -->
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482 <test expect_num_outputs="2">
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483 <conditional name="query|subcommand">
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484 <param name="download_by" value="taxon"/>
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485 <param name="taxon_positional" value="4932"/>
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486 <param name="tax_exact_match" value="true"/>
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487 </conditional>
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488 <output name="genome_data_report">
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489 <assert_contents>
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490 <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>
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491 </assert_contents>
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492 </output>
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493 </test>
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494 <!-- test search filter -->
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495 <test expect_num_outputs="1">
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496 <conditional name="query|subcommand">
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497 <param name="download_by" value="taxon"/>
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498 <param name="taxon_positional" value="Streptococcus"/>
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499 </conditional>
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500 <section name="filters">
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501 <repeat name="search">
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502 <param name="search" value="pyogenes"/>
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503 </repeat>
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504 </section>
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505 <section name="file_choices">
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506 <param name="include" value_json="null"/>
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507 </section>
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508 <output name="genome_data_report">
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509 <assert_contents>
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510 <has_text text="pyogenes"/>
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511 </assert_contents>
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512 </output>
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513 </test>
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514 </tests>
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515 <help><![CDATA[
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516 .. class:: infomark
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517
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518 **What it does**
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519
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520 Downloads genome assemblies from NCBI using the `datasets`_ command-line tool.
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521 Retrieve genome sequences, annotations, and metadata by accession or taxon.
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522
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523 **Query Options**
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524
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525 - **By Accession**: NCBI Assembly (GCF\_/GCA\_) or BioProject accession
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526 - **By Taxon**: Taxonomy ID, scientific name, or common name
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527
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528 **Filters**
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529
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530 ==================== ===============================================
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531 Filter Description
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532 ==================== ===============================================
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533 Reference only Limit to reference/representative assemblies
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534 Annotated only Include only genomes with annotations
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535 Assembly level Chromosome, complete, contig, or scaffold
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536 Assembly source RefSeq (GCF\_) or GenBank (GCA\_)
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537 Exclude atypical Remove atypical assemblies (e.g., partial)
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538 MAG filter Include/exclude metagenome-assembled genomes
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539 Date range Filter by release date
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540 ==================== ===============================================
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541
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542 ----
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543
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544 .. class:: warningmark
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545
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546 **Note**: The "Reference only" filter returns only RefSeq (GCF\_) assemblies.
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547 If a taxon has only GenBank (GCA\_) assemblies, this filter will return no results
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548 with a misleading error message. It is a NCBI datasets bug (not a Galaxy bug).
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549
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550 **Outputs**
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551
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552 - **Data Report**: Tabular metadata for matching assemblies
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553 - **Genome FASTA**: Genomic sequences (nested collection by accession)
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554 - **Annotation files**: GFF3, GTF, GenBank flat files
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555 - **Protein/RNA/CDS**: Amino acid and nucleotide sequences
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556 - **Sequence Report**: Per-sequence metadata (chromosome, length, etc.)
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557
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558 .. _datasets: https://www.ncbi.nlm.nih.gov/datasets/
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559
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560 ]]></help>
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561 <expand macro="citations"/>
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562 </tool>