Mercurial > repos > iuc > ncbi_datasets

annotate datasets_genome.xml @ 10:a3395b1d871b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
author iuc
date Mon, 21 Nov 2022 11:40:05 +0000
parents 18eed8fa7f23
children ac24fff14f23
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0622d99c2619 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210
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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="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 $query.subcommand.tax_exact_match
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19 #end if
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20 $filters.reference
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21 $filters.annotated
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22 #if $filters.assembly_level:
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23 --assembly-level $filters.assembly_level
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24 #end if
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25 --assembly-version $filters.assembly_version
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26 #if $filters.assembly_source:
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27 --assembly-source $filters.assembly_source
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28 #end if
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29 #if $filters.chromosomes:
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30 --chromosomes '$filters.chromosomes'
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31 #end if
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32 $filters.exclude_atypical
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33 @INCLUDE@
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34 @RELEASED_BEFORE@
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35 @RELEASED_AFTER@
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36 #for search_term in $filters.search:
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37 --search '$filters.search_term'
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38 #end for
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39 --no-progressbar
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40 #if $uncompressed
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41 && 7z x -y ncbi_dataset.zip
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42 #else
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43 && 7z l ncbi_dataset.zip > ncbi_dataset.txt
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44 #end if
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45 ]]></command>
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46 <inputs>
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47 <section name="query" title="Query" expanded="true">
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48 <conditional name="subcommand">
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49 <param name="download_by" type="select" label="Choose how to find genomes to download">
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50 <option value="accession">Download by NCBI assembly or BioProject accession</option>
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51 <option value="taxon">Download by taxon</option>
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52 </param>
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53 <when value="accession">
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54 <expand macro="text_or_file"/>
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55 </when>
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56 <when value="taxon">
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57 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."/>
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58 <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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59 </when>
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60 </conditional>
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61 </section>
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62 <section name="filters" title="Filters and Limit">
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63 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
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64 <expand macro="annotation"/>
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65 <expand macro="assembly_level"/>
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66 <param argument="--assembly-version" type="select" label="Assembly version(s)">
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67 <option value="latest">Latest</option>
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68 <option value="all">All</option>
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69 </param>
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70 <!-- TODO add test for assembly source: according to CLI doc args are RefSeq, GenBank, All and not refseq / genbank-->
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71 <expand macro="assembly_source"/>
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72 <expand macro="chromosomes"/>
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73 <param argument="--exclude-atypical" type="boolean" truevalue="--exclude-atypical" falsevalue="" label="Exclude atypical assemblies"/>
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74 <expand macro="released_options"/>
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75 <expand macro="released_options" before_or_after="after"/>
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76
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77 <repeat name="search" title="Add search terms">
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78 <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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79 </repeat>
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80 </section>
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81 <section name="file_choices" title="File Choices" expanded="true">
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82 <expand macro="include"/>
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83 </section>
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84 <param name="uncompressed" type="boolean" label="Uncompress the dataset archive" checked="true"/>
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85 </inputs>
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86 <outputs>
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87 <data name="compressed_archive" format="zip" label="Compressed Archive" from_work_dir="ncbi_dataset.zip">
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88 <filter>not uncompressed</filter>
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89 </data>
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90 <data name="archive_contents" format="txt" label="Archive Contents" from_work_dir="ncbi_dataset.txt">
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91 <filter>not uncompressed</filter>
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92 </data>
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93 <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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94 <filter>uncompressed</filter>
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95 </data>
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96 <collection name="sequence_report" label="NCBI Genome Datasets: Sequence Data Report" type="list">
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97 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
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98 <filter>uncompressed and file_choices['include'] and "seq-report" in file_choices['include']</filter>
0
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99 </collection>
6
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100 <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
10
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101 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)(_genomic)?.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
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102 <filter>uncompressed and file_choices['include'] and "genome" in file_choices['include']</filter>
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103 </collection>
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104 <collection name="rna_fasta" label="NCBI Genome Datasets: RNA fasta" type="list">
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105 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/rna\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
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106 <filter>uncompressed and file_choices['include'] and "rna" in file_choices['include']</filter>
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107 </collection>
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108 <collection name="protein_fasta" label="NCBI Genome Datasets: protein fasta" type="list">
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109 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
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110 <filter>uncompressed and file_choices['include'] and "protein" in file_choices['include']</filter>
0
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111 </collection>
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112 <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
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113 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/cds_from_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"/>
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114 <filter>uncompressed and file_choices['include'] and "cds" in file_choices['include']</filter>
0
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115 </collection>
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116 <collection name="genomic_gff" label="NCBI Genome Datasets: genomic gff3" type="list">
10
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117 <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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118 <filter>uncompressed and file_choices['include'] and "gff3" in file_choices['include']</filter>
0
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119 </collection>
10
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120 <collection name="genomic_gtf" label="NCBI Genome Datasets: gtf" type="list">
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121 <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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122 <filter>uncompressed and file_choices['include'] and "gtf" in file_choices['include']</filter>
0
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123 </collection>
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124 <collection name="genomic_gbff" label="NCBI Genome Datasets: GenBank flatfile" type="list">
10
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125 <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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126 <filter>uncompressed and file_choices['include'] and "gbff" in file_choices['include']</filter>
0
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127 </collection>
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128 </outputs>
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129 <tests>
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130 <test expect_num_outputs="2">
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131 <conditional name="query|subcommand">
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132 <param name="download_by" value="taxon"/>
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133 <param name="text_or_file" value="text"/>
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134 <param name="taxon" value="human"/>
0
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135 </conditional>
10
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136 <param name="chromosomes" value="21"/>
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137 <param name="include" value=""/>
0
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138 <param name="uncompressed" value="false"/>
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139 <param name="released_before" value="01/01/2018"/>
0
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140 <output name="archive_contents">
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141 <assert_contents>
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142 <has_text text="ncbi_dataset/data/dataset_catalog.json"/>
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143 </assert_contents>
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144 </output>
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145 </test>
5
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146 <test expect_num_outputs="2">
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147 <conditional name="query|subcommand">
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148 <param name="download_by" value="taxon"/>
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149 <param name="text_or_file" value="text"/>
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150 <param name="taxon" value="human"/>
5
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151 </conditional>
10
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152 <param name="chromosomes" value="21"/>
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153 <param name="include" value="genome"/>
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154 <param name="uncompressed" value="true"/>
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155 <param name="assembly_level" value="chromosome,complete"/>
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156 <param name="released_before" value="01/01/2018"/>
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157 <output_collection name="genome_fasta" type="list:list" count="14">
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158 <expand macro="genome_fasta_assert" el1="GCA_000002115.2" el2="chr21" expression=">"/>
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159 <expand macro="genome_fasta_assert" el1="GCA_000002125.2" el2="chr21" expression=">"/>
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160 <expand macro="genome_fasta_assert" el1="GCA_000002135.3" el2="GCA_000002135.3_CRA_TCAGchr7v2" expression=">"/>
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161 <expand macro="genome_fasta_assert" el1="GCA_000212995.1" el2="chr21" expression=">"/>
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162 <expand macro="genome_fasta_assert" el1="GCA_000252825.1" el2="chr21" expression=">"/>
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163 <expand macro="genome_fasta_assert" el1="GCA_000306695.2" el2="chr21" expression=">"/>
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164 <expand macro="genome_fasta_assert" el1="GCA_000365445.1" el2="chr21" expression=">"/>
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165 <!-- TODO chromosomes argument (or data) seems not reliable https://github.com/ncbi/datasets/issues/188-->
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166 <expand macro="genome_fasta_assert" el1="GCA_000442335.2" el2="GCA_000442335.2_LinearCen1.1_normalized" expression=">" expression_n="25"/>
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167 <expand macro="genome_fasta_assert" el1="GCA_001292825.2" el2="chr21" expression=">"/>
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168 <expand macro="genome_fasta_assert" el1="GCA_001524155.4" el2="chr21" expression=">"/>
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169 <expand macro="genome_fasta_assert" el1="GCA_001712695.1" el2="chr21" expression=">"/>
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170 <expand macro="genome_fasta_assert" el1="GCA_022833125.2" el2="chr21" expression=">"/>
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171 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
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172 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
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173 </output_collection>
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174 <output name="genome_data_report">
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175 <assert_contents>
10
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176 <has_text text="Homo sapiens"/>
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177 </assert_contents>
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178 </output>
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179 </test>
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180 <!-- same as precious test but assembly_source (refseq which removes some of the genomes) -->
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181 <test expect_num_outputs="2">
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182 <conditional name="query|subcommand">
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183 <param name="download_by" value="taxon"/>
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184 <param name="text_or_file" value="text"/>
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185 <param name="taxon" value="human"/>
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186 </conditional>
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187 <param name="chromosomes" value="21"/>
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188 <param name="include" value="genome"/>
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189 <param name="uncompressed" value="true"/>
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190 <param name="assembly_level" value="chromosome,complete"/>
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191 <param name="assembly_source" value="refseq"/>
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192 <param name="released_before" value="01/01/2018"/>
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193 <output_collection name="genome_fasta" type="list:list" count="2">
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194 <expand macro="genome_fasta_assert" el1="GCF_000002125.1" el2="chr21" expression=">"/>
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195 <expand macro="genome_fasta_assert" el1="GCF_000306695.2" el2="chr21" expression=">"/>
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196 </output_collection>
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197 <output name="genome_data_report">
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198 <assert_contents>
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199 <has_text text="Homo sapiens"/>
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200 </assert_contents>
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201 </output>
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202 </test>
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203 <test expect_num_outputs="4">
0
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204 <conditional name="query|subcommand">
10
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205 <param name="download_by" value="accession"/>
0
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206 <conditional name="text_or_file">
10
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207 <param name="text_or_file" value="text"/>
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208 <param name="accession" value="GCF_000013305.1 GCF_000007445.1"/>
0
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209 </conditional>
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210 </conditional>
10
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211 <param name="include" value="seq-report,gtf,cds"/>
0
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212 <param name="uncompressed" value="true"/>
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213 <param name="released_before" value="01/01/2007"/>
0
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214 <output name="genome_data_report">
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215 <assert_contents>
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216 <has_text text="GCF_000013305.1"/>
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217 </assert_contents>
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218 </output>
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219 <output_collection name="genomic_gtf" type="list">
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220 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
0
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221 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.gtf" compare="contains"/>
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222 </output_collection>
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223 <output_collection name="genomic_cds" type="list">
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224 <element name="GCF_000007445.1" file="genome.2.GCF_000007445.1.genomic.cds" compare="contains"/>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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225 <element name="GCF_000013305.1" file="genome.2.GCF_000013305.1.genomic.cds" compare="contains"/>
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226 </output_collection>
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227 </test>
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228 <test expect_num_outputs="4">
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229 <conditional name="query|subcommand">
10
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230 <param name="download_by" value="accession"/>
0
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231 <conditional name="text_or_file">
10
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232 <param name="text_or_file" value="file"/>
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233 <param name="inputfile" value="accessions.txt"/>
0
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234 </conditional>
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235 </conditional>
10
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236 <param name="include" value="seq-report,gbff,gff3"/>
0
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237 <param name="uncompressed" value="true"/>
10
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238 <param name="released_before" value="01/01/2007"/>
0
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239 <output name="genome_data_report">
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240 <assert_contents>
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241 <has_text text="SAMN02604181"/>
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242 </assert_contents>
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243 </output>
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244 <output_collection name="genomic_gff" type="list">
9
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245 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gff" compare="contains"/>
0
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246 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gff" compare="contains"/>
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247 </output_collection>
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248 <output_collection name="genomic_gbff" type="list">
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249 <element name="GCF_000007445.1" file="genome.3.GCF_000007445.1.genomic.gbff" compare="contains"/>
0
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250 <element name="GCF_000013305.1" file="genome.3.GCF_000013305.1.genomic.gbff" compare="contains"/>
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251 </output_collection>
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252 </test>
5
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253 <test expect_num_outputs="2">
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254 <conditional name="query|subcommand">
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255 <param name="download_by" value="accession"/>
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256 <conditional name="text_or_file">
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257 <param name="text_or_file" value="text"/>
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258 <param name="accession" value="GCF_000001405"/>
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259 </conditional>
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260 </conditional>
10
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261 <param name="include" value="seq-report"/>
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262 <param name="uncompressed" value="true"/>
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263 <param name="released_before" value="01/01/2015"/>
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264 <param name="assembly_version" value="all"/>
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265 <output_collection name="sequence_report" count="4">
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266 <element name="GCF_000001405.25">
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267 <assert_contents>
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268 <has_text text="assignedMoleculeLocationType"/>
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269 </assert_contents>
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270 </element>
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271 <element name="GCF_000001405.26">
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272 <assert_contents>
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273 <has_text text="assignedMoleculeLocationType"/>
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274 </assert_contents>
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275 </element>
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276 <element name="GCF_000001405.27">
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277 <assert_contents>
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278 <has_text text="assignedMoleculeLocationType"/>
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279 </assert_contents>
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280 </element>
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281 <element name="GCF_000001405.28">
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282 <assert_contents>
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283 <has_text text="assignedMoleculeLocationType"/>
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284 </assert_contents>
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285 </element>
5
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286 </output_collection>
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287 </test>
7
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288 <test expect_num_outputs="5">
6
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289 <conditional name="query|subcommand">
10
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290 <param name="download_by" value="accession"/>
6
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291 <conditional name="text_or_file">
10
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292 <param name="text_or_file" value="text"/>
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293 <param name="accession" value="GCF_000146045.2"/>
6
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294 </conditional>
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295 </conditional>
10
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296 <param name="include" value="seq-report,genome,rna,cds"/>
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297 <param name="uncompressed" value="true"/>
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298 <output_collection name="genome_fasta" type="list:list" count="1">
10
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299 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
6
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300 </output_collection>
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301 </test>
8
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302 <test expect_num_outputs="3">
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303 <conditional name="query|subcommand">
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304 <param name="download_by" value="accession"/>
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305 <conditional name="text_or_file">
10
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306 <param name="text_or_file" value="text"/>
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307 <param name="accession" value="GCF_000146045.2 GCF_000002945.1"/>
8
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308 </conditional>
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309 </conditional>
10
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310 <param name="include" value="seq-report,genome"/>
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311 <param name="uncompressed" value="true"/>
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312 <output_collection name="genome_fasta" type="list:list" count="2">
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313 <expand macro="genome_fasta_assert" el1="GCF_000002945.1" el2="GCF_000002945.1_ASM294v2" expression=">NC_[0-9]+\.[0-9]+ Schizosaccharomyces pombe (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="4"/>
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314 <expand macro="genome_fasta_assert" el1="GCF_000146045.2" el2="GCF_000146045.2_R64" expression=">NC_[0-9]+\.[0-9]+ Saccharomyces cerevisiae S288[Cc] (mitochondrion|chromosome .*), complete (sequence|genome)" expression_n="17"/>
8
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315 </output_collection>
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316 </test>
10
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317 <!-- tax_exact_match seems not able to filter out strains
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318 https://github.com/ncbi/datasets/issues/187
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319 hence we set expect_test_failure="true"-->
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320 <test expect_num_outputs="1" expect_test_failure="true">
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321 <conditional name="query|subcommand">
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322 <param name="download_by" value="taxon"/>
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323 <param name="text_or_file" value="text"/>
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324 <param name="taxon" value="4932"/>
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325 <param name="tax_exact_match" value="true"/>
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326 </conditional>
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327 <param name="include" value=""/>
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328 <param name="uncompressed" value="true"/>
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329 <output name="genome_data_report">
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330 <assert_contents>
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331 <has_text text="Saccharomyces cerevisiae ZTW1" negate="true"/>
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332 </assert_contents>
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333 </output>
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334 </test>
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335 </tests>
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336 <help>
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337 <![CDATA[
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338 **Download Genome Datasets from NCBI**
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339
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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340 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
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341 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
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342
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343 Tthe default genome dataset includes the following files (if available):
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344 * data_report.jsonl (genome assembly and annotation metadata, not always available)
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345 * genomic.fna (genomic sequences)
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346 * rna.fna (transcript sequences)
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347 * protein.faa (protein sequences)
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348 * genomic.gff (genome annotation in gff3 format)
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349 * dataset_catalog.json (a list of files and file types included in the dataset)
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350 ]]>
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351 </help>
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352
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353 </tool>