Mercurial > repos > iuc > ncbi_datasets

annotate datasets_genome.xml @ 0:c6009f4d7261 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
author iuc
date Thu, 15 Jul 2021 13:31:56 +0000
parents
children 2753a5786114
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0
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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1 <tool id="datasets-download-genome" name="NCBI datasets download genome" profile="@PROFILE@" license="@LICENSE" version="@TOOL_VERSION@">
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2 <description>Download assembled genomes from NCBI</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 $subcommand.download_by
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10 #if $subcommand.download_by == 'accession':
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11 #if $subcommand.text_or_file.text_or_file == 'text':
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12 '$subcommand.text_or_file.accession'
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13 #else
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14 --inputfile '$subcommand.text_or_file.inputfile'
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15 #end if
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16 #else:
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17 '$subcommand.taxon'
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18 #end if
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19 $annotated
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20 $dehydrated
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21 #if $assembly_level:
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22 --assembly_level $assembly_level
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23 #end if
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24 #if $assembly_source:
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25 --assembly_source $assembly_source
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26 #end if
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27 --chromosomes '$chromosomes'
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28 @EXCLUDES_GENOME@
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29 @INCLUDES_GENOME@
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30 $reference
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31 @RELEASED_BEFORE@
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32 @RELEASED_SINCE@
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33 #for search_term in $search:
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34 --search '$search_term'
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35 #end for
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36 #if not $dehydrated:
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37 && 7z x ncbi_dataset.zip
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38 #end if
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39 ]]></command>
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40 <inputs>
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41 <conditional name="subcommand">
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42 <param name="download_by" type="select" label="Choose how to find genomes to download">
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43 <option value="accession">Download by NCBI assembly or BioProject accession</option>
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44 <option value="taxon">Download by taxon</option>
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45 </param>
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46 <when value="accession">
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47 <expand macro="text_or_file"/>
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48 </when>
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49 <when value="taxon">
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50 <param name="taxon" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurs, etc."></param>
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51 </when>
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52 </conditional>
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53 <expand macro="annotation"></expand>
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54 <expand macro="dehydrated"></expand>
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55 <expand macro="assembly_level"></expand>
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56 <expand macro="assembly_source"></expand>
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57 <expand macro="chromosomes"></expand>
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58 <expand macro="excludes_genome"></expand>
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59 <expand macro="includes_genome"></expand>
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60 <expand macro="released_options"></expand>
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61 <expand macro="released_options" before_or_after="since"></expand>
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62 <param argument="--reference" type="boolean" truevalue="--reference" falsevalue="" label="Limit to reference and representative (GCF_ and GCA_) assemblies"/>
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63 <repeat name="search" title="Add search terms">
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64 <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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65 </repeat>
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66 </inputs>
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67 <outputs>
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68 <data name="dehydrated_archive" format="zip" label="Dehydrated Archive" from_work_dir="ncbi_dataset.zip">
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69 <filter>dehydrated</filter>
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70 </data>
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71 <collection name="genome_fasta" label="NCBI genome datasets: genome fasta" type="list">
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72 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/.*_genomic\.fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
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73 <filter>not dehydrated and not exclude_seq</filter>
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74 </collection>
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75 <collection name="protein_fasta" label="NCBI genome datasets: protein fasta" type="list">
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76 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/protein\.faa" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
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77 <filter>not dehydrated and not exclude_protein</filter>
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78 </collection>
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79 <collection name="genomic_gff" label="NCBI genome datasets: genomic gff" type="list">
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80 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gff" ext="gff3" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
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81 <filter>not dehydrated and not exclude_gff3</filter>
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82 </collection>
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83 <collection name="genomic_gtf" label="NCBI genome datasets: genomic gtf" type="list">
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84 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gtf" ext="gtf" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
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85 <filter>not dehydrated and include_gtf</filter>
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86 </collection>
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87 <collection name="genomic_gbff" label="NCBI genome datasets: genomic gbff" type="list">
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88 <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/genomic\.gbff" ext="genbank" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
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89 <filter>not dehydrated and include_gbff</filter>
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90 </collection>
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91 </outputs>
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92 <tests>
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93 <test title="test dehydrated download by taxon">
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94 <conditional name="subcommand">
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95 <param name="download_by" value="taxon"></param>
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96 <param name="text_or_file" value="text"></param>
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97 <param name="taxon" value="human"></param>
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98 </conditional>
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99 <param name="chromosomes" value="21"></param>
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100 <param name="dehydrated" value="true"/>
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101 <param name="released_before" value="01/01/2018"></param>
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102 <output name="dehydrated_archive" value="human_chrom_21_dehydrated.zip" compare="sim_size" delta="10000"/>
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103 </test>
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104 <test title="test download by comma-separated accession">
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105 <conditional name="subcommand">
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106 <param name="download_by" value="accession"></param>
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107 <conditional name="text_or_file">
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108 <param name="text_or_file" value="text"></param>
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109 <param name="accession" value="GCF_000013305.1,GCF_000007445.1"></param>
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110 </conditional>
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111 </conditional>
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112 <param name="dehydrated" value="false"/>
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113 <param name="released_before" value="01/01/2007"></param>
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114 <output_collection name="genome_fasta" type="list">
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115 <element name="GCF_000013305.1" file="GCF_000013305.1.genome.fa" compare="contains"/>
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116 <element name="GCF_000007445.1" file="GCF_000007445.1.genome.fa" compare="contains"/>
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117 </output_collection>
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118 <output_collection name="protein_fasta" type="list">
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119 <element name="GCF_000013305.1" file="GCF_000013305.1.protein.fa" compare="contains"/>
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120 <element name="GCF_000007445.1" file="GCF_000007445.1.protein.fa" compare="contains"/>
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121 </output_collection>
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122 <output_collection name="genomic_gff" type="list">
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123 <element name="GCF_000013305.1" file="GCF_000013305.1.genomic.gff" compare="contains"/>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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124 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gff" compare="contains"/>
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125 </output_collection>
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126 </test>
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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127 <test title="test download by accessions listed in file">
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128 <conditional name="subcommand">
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129 <param name="download_by" value="accession"></param>
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130 <conditional name="text_or_file">
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131 <param name="text_or_file" value="file"></param>
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132 <param name="inputfile" value="accessions.txt"></param>
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133 </conditional>
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134 </conditional>
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135 <param name="include_gbff" value="true"/>
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136 <param name="include_gtf" value="true"/>
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137 <param name="dehydrated" value="false"/>
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138 <param name="released_before" value="01/01/2007"></param>
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139 <output_collection name="genome_fasta" type="list">
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140 <element name="GCF_000013305.1" file="GCF_000013305.1.genome.fa" compare="contains"/>
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141 <element name="GCF_000007445.1" file="GCF_000007445.1.genome.fa" compare="contains"/>
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142 </output_collection>
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143 <output_collection name="protein_fasta" type="list">
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144 <element name="GCF_000013305.1" file="GCF_000013305.1.protein.fa" compare="contains"/>
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145 <element name="GCF_000007445.1" file="GCF_000007445.1.protein.fa" compare="contains"/>
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146 </output_collection>
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147 <output_collection name="genomic_gff" type="list">
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148 <element name="GCF_000013305.1" file="GCF_000013305.1.genomic.gff" compare="contains"/>
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149 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gff" compare="contains"/>
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150 </output_collection>
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151 <output_collection name="genomic_gtf" type="list">
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152 <element name="GCF_000013305.1" file="GCF_000013305.1.genomic.gtf" compare="contains"/>
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153 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gtf" compare="contains"/>
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154 </output_collection>
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155 <output_collection name="genomic_gbff" type="list">
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156 <element name="GCF_000013305.1" file="GCF_000013305.1.genomic.gbff" compare="contains"/>
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157 <element name="GCF_000007445.1" file="GCF_000007445.1.genomic.gbff" compare="contains"/>
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158 </output_collection>
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159 </test>
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160 </tests>
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161 <help>
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162
c6009f4d7261 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit fd91cf3000d556d8219426eddb8a3059071a2009"
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163 Download a genome dataset including genome, transcript and protein sequence, annotation and a detailed data report.
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164 Genome datasets can be specified by NCBI Assembly or BioProject accession or taxon. Datasets are downloaded as a zip file.
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165
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166 The default genome dataset includes the following files (if available):
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167 * genomic.fna (genomic sequences)
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168 * rna.fna (transcript sequences)
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169 * protein.faa (protein sequences)
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170 * genomic.gff (genome annotation in gff3 format)
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171 * data_report.jsonl (data report with genome assembly and annotation metadata)
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172 * dataset_catalog.json (a list of files and file types included in the dataset)
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173 </help>
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174
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175 </tool>