Mercurial > repos > iuc > ncbi_datasets

annotate macros.xml @ 16:a6a475ed58cb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 9a34ebfc4d6b987b71e545dcf5dbdd884cd8d88e
author iuc
date Fri, 07 Jun 2024 14:19:58 +0000
parents 198c75abbf55
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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1 <macros>
16
a6a475ed58cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 9a34ebfc4d6b987b71e545dcf5dbdd884cd8d88e
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2 <token name="@TOOL_VERSION@">16.20.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">23.0</token>
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5 <token name="@LICENSE@">MIT</token>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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6 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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7 <token name="@SETUP_CERTIFICATES@"><![CDATA[
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8 ## If running in a container use certificates from ca-certificates instead of outdated/missing container certificates
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9 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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10 ]]></token>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
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14 <requirement type="package" version="2024.2.2">ca-certificates</requirement>
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15 <requirement type="package" version="16.02">p7zip</requirement>
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16 </requirements>
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17 </xml>
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18 <xml name="bio_tools">
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19 <xrefs>
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20 <xref type="bio.tools">ncbi_datasets</xref>
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21 </xrefs>
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22 </xml>
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23 <xml name="version_command"><![CDATA[
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24 datasets --version | cut -d" " -f 3
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25 ]]></xml>
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26 <xml name="annotation">
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27 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
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28 </xml>
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29 <xml name="assembly_level">
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30 <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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31 <option value="chromosome">Chromosome</option>
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32 <option value="complete">Complete Genome</option>
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33 <option value="contig">Contig</option>
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34 <option value="scaffold">Scaffold</option>
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35 </param>
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36 </xml>
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37 <xml name="assembly_source">
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38 <param argument="--assembly-source" type="select" optional="true" label="Assembly source" help="Default (nothing selected) is both " >
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39 <option value="refseq">RefSeq</option>
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40 <option value="genbank">GenBank</option>
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41 </param>
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42 </xml>
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43 <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession">
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44 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
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45 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
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46 <option value="text">Enter @WHAT@s</option>
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47 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
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48 </param>
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49 <when value="text">
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50 <!-- command section also allows spaces as separator for backward compatibility
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51 prefer comma because this is used also in other text params-->
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52 <param name="accession" type="text" label="Enter comma separated list of @WHAT@s" help="@HELP@">
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53 <validator type="length" min="1" message="Provide at least one @WHAT@"/>
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54 </param>
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55 </when>
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56 <when value="file">
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57 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
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58 </when>
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59 </conditional>
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60 </xml>
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61 <xml name="chromosomes">
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62 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
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63 <sanitizer invalid_char="">
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64 <valid initial="string.letters,string.digits">
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65 <add value="_" />
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66 <add value="." />
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67 <add value="," />
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68 </valid>
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69 </sanitizer>
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70 </param>
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71 </xml>
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73 <xml name="taxon_positional">
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74 <param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, house mouse, bos taurus, etc. or use Taxonomy ID from NCBI for greater accuracy, use species-level only not genera or larger taxa"/>
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75 </xml>
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77 <xml name="ortholog">
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78 <param argument="--ortholog" type="text" label="Retrieve orthologs for taxa" help="Retrieve data for an ortholog set. Provide one or more comma separated taxa (any rank) to filter results or 'all' for the complete set.">
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79 <sanitizer invalid_char="">
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80 <valid initial="string.letters,string.digits">
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81 <add value=" " />
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82 <add value="," />
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83 <add value="-" />
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84 </valid>
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85 </sanitizer>
10
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86 </param>
0
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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87 </xml>
11
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88
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89 <xml name="include">
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90 <param argument="--include" type="select" multiple="true" optional="true" label="Include" help="Download the following datasets (if available)">
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91 <yield/>
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92 </param>
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93 </xml>
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94 <xml name="genome_includes">
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95 <option value="genome" selected="true">genomic sequence (genome)</option>
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96 <option value="rna">transcript (rna)</option>
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97 <option value="protein">amnio acid sequences (protein)</option>
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98 <option value="cds">nucleotide coding sequences (cds)</option>
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99 <option value="gff3">general feature file (gff3)</option>
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100 <option value="gtf">gene transfer format (gtf)</option>
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101 <option value="gbff">GenBank flat file (gbff)</option>
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102 <option value="seq-report">sequence report file (seq-report)</option>
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103 <yield/>
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104 </xml>
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105 <xml name="gene_includes">
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106 <option value="gene">gene sequence (gene)</option>
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107 <option value="protein" selected="true">amnio acid sequences (protein)</option>
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108 <yield/>
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109 </xml>
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110
10
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111 <token name="@INCLUDE@"><![CDATA[
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112 --include
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113 #if $file_choices.include
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114 #echo ",".join($file_choices.include)
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115 #else
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116 none
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117 #end if
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118 ]]></token>
11
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119 <xml name="tsv_report_columns">
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120 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
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121 <option value="accession">Assembly Accession</option>
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122 <option value="annotinfo-busco-complete">Annotation BUSCO Complete</option>
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123 <option value="annotinfo-busco-duplicated">Annotation BUSCO Duplicated</option>
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124 <option value="annotinfo-busco-fragmented">Annotation BUSCO Fragmented</option>
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125 <option value="annotinfo-busco-lineage">Annotation BUSCO Lineage</option>
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126 <option value="annotinfo-busco-missing">Annotation BUSCO Missing</option>
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127 <option value="annotinfo-busco-singlecopy">Annotation BUSCO Single Copy</option>
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128 <option value="annotinfo-busco-totalcount">Annotation BUSCO Total Count</option>
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129 <option value="annotinfo-busco-ver">Annotation BUSCO Version</option>
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130 <option value="annotinfo-featcount-gene-non-coding">Annotation Count Gene Non-coding</option>
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131 <option value="annotinfo-featcount-gene-other">Annotation Count Gene Other</option>
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132 <option value="annotinfo-featcount-gene-protein-coding">Annotation Count Gene Protein-coding</option>
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133 <option value="annotinfo-featcount-gene-pseudogene">Annotation Count Gene Pseudogene</option>
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134 <option value="annotinfo-featcount-gene-total">Annotation Count Gene Total</option>
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135 <option value="annotinfo-method">Annotation Method</option>
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136 <option value="annotinfo-name">Annotation Name</option>
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137 <option value="annotinfo-pipeline">Annotation Pipeline</option>
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138 <option value="annotinfo-provider">Annotation Provider</option>
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139 <option value="annotinfo-release-date">Annotation Release Date</option>
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140 <option value="annotinfo-release-version">Annotation Release Version</option>
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141 <option value="annotinfo-report-url">Annotation Report URL</option>
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142 <option value="annotinfo-software-version">Annotation Software Version</option>
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143 <option value="annotinfo-status">Annotation Status</option>
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144 <option value="assminfo-atypicalis-atypical">Assembly Atypical Is Atypical</option>
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145 <option value="assminfo-atypicalwarnings">Assembly Atypical Warnings</option>
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146 <option value="assminfo-bioproject-lineage-accession">Assembly BioProject Lineage Accession</option>
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147 <option value="assminfo-bioproject-lineage-parent-accession">Assembly BioProject Lineage Parent Accession</option>
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148 <option value="assminfo-bioproject-lineage-parent-accessions">Assembly BioProject Lineage Parent Accessions</option>
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149 <option value="assminfo-bioproject-lineage-title">Assembly BioProject Lineage Title</option>
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150 <option value="assminfo-biosample-accession">Assembly BioSample Accession</option>
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151 <option value="assminfo-biosample-attribute-name">Assembly BioSample Attribute Name</option>
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152 <option value="assminfo-biosample-attribute-value">Assembly BioSample Attribute Value</option>
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153 <option value="assminfo-biosample-bioproject-accession">Assembly BioSample BioProject Accession</option>
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154 <option value="assminfo-biosample-bioproject-parent-accession">Assembly BioSample BioProject Parent Accession</option>
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155 <option value="assminfo-biosample-bioproject-parent-accessions">Assembly BioSample BioProject Parent Accessions</option>
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156 <option value="assminfo-biosample-bioproject-title">Assembly BioSample BioProject Title</option>
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157 <option value="assminfo-biosample-description-comment">Assembly BioSample Description Comment</option>
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158 <option value="assminfo-biosample-description-organism-common-name">Assembly BioSample Description Organism Common Name</option>
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159 <option value="assminfo-biosample-description-organism-infraspecific-breed">Assembly BioSample Description Organism Infraspecific Names Breed</option>
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160 <option value="assminfo-biosample-description-organism-infraspecific-cultivar">Assembly BioSample Description Organism Infraspecific Names Cultivar</option>
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161 <option value="assminfo-biosample-description-organism-infraspecific-ecotype">Assembly BioSample Description Organism Infraspecific Names Ecotype</option>
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162 <option value="assminfo-biosample-description-organism-infraspecific-isolate">Assembly BioSample Description Organism Infraspecific Names Isolate</option>
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163 <option value="assminfo-biosample-description-organism-infraspecific-sex">Assembly BioSample Description Organism Infraspecific Names Sex</option>
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164 <option value="assminfo-biosample-description-organism-infraspecific-strain">Assembly BioSample Description Organism Infraspecific Names Strain</option>
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165 <option value="assminfo-biosample-description-organism-name">Assembly BioSample Description Organism Name</option>
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166 <option value="assminfo-biosample-description-organism-pangolin">Assembly BioSample Description Organism Pangolin Classification</option>
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167 <option value="assminfo-biosample-description-organism-tax-id">Assembly BioSample Description Organism Taxonomic ID</option>
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168 <option value="assminfo-biosample-description-title">Assembly BioSample Description Title</option>
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169 <option value="assminfo-biosample-ids-db">Assembly BioSample Sample Identifiers Database</option>
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170 <option value="assminfo-biosample-ids-label">Assembly BioSample Sample Identifiers Label</option>
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171 <option value="assminfo-biosample-ids-value">Assembly BioSample Sample Identifiers Value</option>
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172 <option value="assminfo-biosample-last-updated">Assembly BioSample Last updated</option>
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173 <option value="assminfo-biosample-models">Assembly BioSample Models</option>
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174 <option value="assminfo-biosample-owner-contact-lab">Assembly BioSample Owner Contact Lab</option>
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175 <option value="assminfo-biosample-owner-name">Assembly BioSample Owner Name</option>
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176 <option value="assminfo-biosample-package">Assembly BioSample Package</option>
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177 <option value="assminfo-biosample-publication-date">Assembly BioSample Publication date</option>
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178 <option value="assminfo-biosample-status-status">Assembly BioSample Status Status</option>
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179 <option value="assminfo-biosample-status-when">Assembly BioSample Status When</option>
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180 <option value="assminfo-biosample-submission-date">Assembly BioSample Submission date</option>
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181 <option value="assminfo-blast-url">Assembly Blast URL</option>
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182 <option value="assminfo-description">Assembly Description</option>
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183 <option value="assminfo-level">Assembly Level</option>
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184 <option value="assminfo-linked-assmaccession">Assembly Linked Assembly Accession</option>
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185 <option value="assminfo-linked-assmtype">Assembly Linked Assembly Type</option>
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186 <option value="assminfo-name">Assembly Name</option>
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187 <option value="assminfo-paired-assmaccession">Assembly Paired Assembly Accession</option>
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188 <option value="assminfo-paired-assmname">Assembly Paired Assembly Name</option>
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189 <option value="assminfo-paired-assmstatus">Assembly Paired Assembly Status</option>
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190 <option value="assminfo-refseq-category">Assembly Refseq Category</option>
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191 <option value="assminfo-sequencing-tech">Assembly Sequencing Tech</option>
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192 <option value="assminfo-status">Assembly Status</option>
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193 <option value="assminfo-submission-date">Assembly Submission Date</option>
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194 <option value="assminfo-submitter">Assembly Submitter</option>
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195 <option value="assminfo-synonym">Assembly Synonym</option>
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196 <option value="assminfo-type">Assembly Type</option>
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197 <option value="assmstats-contig-l50">Assembly Stats Contig L50</option>
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198 <option value="assmstats-contig-n50">Assembly Stats Contig N50</option>
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199 <option value="assmstats-gaps-between-scaffolds-count">Assembly Stats Gaps Between Scaffolds Count</option>
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200 <option value="assmstats-gc-count">Assembly Stats GC Count</option>
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201 <option value="assmstats-gc-percent">Assembly Stats GC Percent</option>
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202 <option value="assmstats-number-of-component-sequences">Assembly Stats Number of Component Sequences</option>
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203 <option value="assmstats-number-of-contigs">Assembly Stats Number of Contigs</option>
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204 <option value="assmstats-number-of-scaffolds">Assembly Stats Number of Scaffolds</option>
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205 <option value="assmstats-scaffold-l50">Assembly Stats Scaffold L50</option>
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206 <option value="assmstats-scaffold-n50">Assembly Stats Scaffold N50</option>
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207 <option value="assmstats-total-number-of-chromosomes">Assembly Stats Total Number of Chromosomes</option>
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208 <option value="assmstats-total-sequence-len">Assembly Stats Total Sequence Length</option>
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209 <option value="assmstats-total-ungapped-len">Assembly Stats Total Ungapped Length</option>
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210 <option value="current-accession">Current Accession</option>
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211 <option value="organelle-assembly-name">Organelle Assembly Name</option>
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212 <option value="organelle-bioproject-accessions">Organelle BioProject Accessions</option>
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213 <option value="organelle-description">Organelle Description</option>
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214 <option value="organelle-infraspecific-name">Organelle Infraspecific Name</option>
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215 <option value="organelle-submitter">Organelle Submitter</option>
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216 <option value="organelle-total-seq-length">Organelle Total Seq Length</option>
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217 <option value="organism-common-name">Organism Common Name</option>
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218 <option value="organism-infraspecific-breed">Organism Infraspecific Names Breed</option>
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219 <option value="organism-infraspecific-cultivar">Organism Infraspecific Names Cultivar</option>
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220 <option value="organism-infraspecific-ecotype">Organism Infraspecific Names Ecotype</option>
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221 <option value="organism-infraspecific-isolate">Organism Infraspecific Names Isolate</option>
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222 <option value="organism-infraspecific-sex">Organism Infraspecific Names Sex</option>
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223 <option value="organism-infraspecific-strain">Organism Infraspecific Names Strain</option>
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224 <option value="organism-name">Organism Name</option>
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225 <option value="organism-pangolin">Organism Pangolin Classification</option>
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226 <option value="organism-tax-id">Organism Taxonomic ID</option>
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227 <option value="source_database">Source Database</option>
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228 <option value="wgs-contigs-url">WGS contigs URL</option>
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229 <option value="wgs-project-accession">WGS project accession</option>
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230 <option value="wgs-url">WGS URL</option>
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231 <yield/>
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232 </param>
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233 </xml>
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234
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235 <xml name="gene_tsv_report_columns">
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236 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
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237 <option value="annotation-assembly-accession">Annotation Assembly Accession</option>
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238 <option value="annotation-assembly-name">Annotation Assembly Name</option>
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239 <option value="annotation-genomic-range-accession">Annotation Genomic Range Accession</option>
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240 <option value="annotation-genomic-range-exon-order">Annotation Genomic Range Exons Order</option>
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241 <option value="annotation-genomic-range-exon-orientation">Annotation Genomic Range Exons Orientation</option>
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242 <option value="annotation-genomic-range-exon-start">Annotation Genomic Range Exons Start</option>
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243 <option value="annotation-genomic-range-exon-stop">Annotation Genomic Range Exons Stop</option>
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244 <option value="annotation-genomic-range-range-order">Annotation Genomic Range Order</option>
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245 <option value="annotation-genomic-range-range-orientation">Annotation Genomic Range Orientation</option>
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246 <option value="annotation-genomic-range-range-start">Annotation Genomic Range Start</option>
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247 <option value="annotation-genomic-range-range-stop">Annotation Genomic Range Stop</option>
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248 <option value="annotation-genomic-range-seq-name">Annotation Genomic Range Seq Name</option>
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249 <option value="annotation-release-date">Annotation Release Date</option>
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250 <option value="annotation-release-name">Annotation Release Name</option>
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251 <option value="chromosomes">Chromosomes</option>
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252 <option value="common-name">Common Name</option>
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253 <option value="description">Description</option>
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254 <option value="ensembl-geneids">Ensembl GeneIDs</option>
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255 <option value="gene-id">NCBI GeneID</option>
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256 <option value="gene-type">Gene Type</option>
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257 <option value="genomic-region-gene-range-accession">Genomic Region Gene Range Sequence Accession</option>
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258 <option value="genomic-region-gene-range-range-order">Genomic Region Gene Range Order</option>
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259 <option value="genomic-region-gene-range-range-orientation">Genomic Region Gene Range Orientation</option>
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260 <option value="genomic-region-gene-range-range-start">Genomic Region Gene Range Start</option>
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261 <option value="genomic-region-gene-range-range-stop">Genomic Region Gene Range Stop</option>
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262 <option value="genomic-region-genomic-region-type">Genomic Region Genomic Region Type</option>
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263 <option value="group-id">Gene Group Identifier</option>
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264 <option value="group-method">Gene Group Method</option>
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265 <option value="name-authority">Nomenclature Authority</option>
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266 <option value="name-id">Nomenclature ID</option>
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267 <option value="omim-ids">OMIM IDs</option>
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268 <option value="orientation">Orientation</option>
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269 <option value="ref-standard-gene-range-accession">Reference Standard Gene Range Sequence Accession</option>
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270 <option value="ref-standard-gene-range-range-order">Reference Standard Gene Range Order</option>
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271 <option value="ref-standard-gene-range-range-orientation">Reference Standard Gene Range Orientation</option>
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272 <option value="ref-standard-gene-range-range-start">Reference Standard Gene Range Start</option>
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273 <option value="ref-standard-gene-range-range-stop">Reference Standard Gene Range Stop</option>
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274 <option value="ref-standard-genomic-region-type">Reference Standard Genomic Region Type</option>
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275 <option value="replaced-gene-id">Replaced NCBI GeneID</option>
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276 <option value="rna-type">RNA Type</option>
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277 <option value="swissprot-accessions">SwissProt Accessions</option>
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278 <option value="symbol">Symbol</option>
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279 <option value="synonyms">Synonyms</option>
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280 <option value="tax-id">Taxonomic ID</option>
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281 <option value="tax-name">Taxonomic Name</option>
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282 <yield/>
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283 </param>
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284 </xml>
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285 <xml name="prok_gene_tsv_report_columns">
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286 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
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287 <option value="accession">Accession</option>
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288 <option value="description">Description</option>
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289 <option value="ec-number">EC Number</option>
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290 <option value="gene-symbol">Gene Symbol</option>
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291 <option value="mapping-count">Number of Genome Mappings</option>
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292 <option value="name-evidence-accession">Protein Name EvidenceAccession</option>
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293 <option value="name-evidence-category">Protein Name EvidenceCategory</option>
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294 <option value="name-evidence-source">Protein Name EvidenceSource</option>
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295 <option value="protein-length">Protein Length</option>
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296 <option value="protein-name">Protein Name</option>
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297 <yield/>
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298 </param>
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299 </xml>
0
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300 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
10
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301 <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)">
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302 <validator type="regex" message="enter a date in the form MM/DD/YYYY">[0-9]{2}/[0-9]{2}/[0-9]{4}</validator>
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303 </param>
0
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304 </xml>
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305 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
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306 --released-before '$filters.released_before'
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307 #end if
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308 </token>
10
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309 <token name="@RELEASED_AFTER@">#if $filters.released_after:
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310 --released-after '$filters.released_after'
0
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311 #end if
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312 </token>
11
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313 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_ftype="fasta" token_expression_n="1">
10
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314 <element name="@EL1@">
11
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315 <element name="@EL2@" ftype="@FTYPE@" decompress="true">
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316 <assert_contents>
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317 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/>
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318 </assert_contents>
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319 </element>
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320 </element>
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321 </xml>
13
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322 <xml name="citations">
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323 <citations>
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324 <citation type="bibtex">@misc{NCBI,
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325 author = "{NCBI}",
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326 title = "NCBI Datasets",
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327 year = "2022",
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328 url = "https://github.com/ncbi/datasets"}
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329 </citation>
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330 </citations>
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331 </xml>
0
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332 </macros>