Mercurial > repos > iuc > ncbi_datasets

annotate macros.xml @ 9:18eed8fa7f23 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit baddca770f8ae8475785374d883b3b42fac27c0c
author iuc
date Wed, 24 Aug 2022 13:00:58 +0000
parents b2ae7186d41f
children a3395b1d871b
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1 <macros>
9
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2 <token name="@TOOL_VERSION@">13.35.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">21.01</token>
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5 <token name="@LICENSE@">MIT</token>
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6 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
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7 <token name="@SETUP_CERTIFICATES@"><![CDATA[
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8 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates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";
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10 ]]></token>
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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="2022.6.15">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="annotation">
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19 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
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20 </xml>
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21 <xml name="dehydrated">
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22 <param argument="--dehydrated" type="boolean" truevalue="--dehydrated" falsevalue="" label="Download a dehydrated zip archive including the data report and locations of data files ?" help="Use the rehydrate tools to retrieve data files"/>
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23 </xml>
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24 <xml name="assembly_level">
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25 <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true">
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26 <option value="chromosome">Chromosome</option>
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27 <option value="complete_genome">Complete Genome</option>
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28 <option value="contig">Contig</option>
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29 <option value="scaffold">Scaffold</option>
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30 </param>
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31 </xml>
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32 <xml name="assembly_source">
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33 <param argument="--assembly-source" type="select" optional="true">
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34 <option value="refseq">RefSeq</option>
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35 <option value="genabnk">GenBank</option>
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36 </param>
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37 </xml>
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38 <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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39 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
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40 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
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41 <option value="text">Enter @WHAT@s</option>
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42 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
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43 </param>
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44 <when value="text">
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45 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@">
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46 <yield/>
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47 </param>
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48 </when>
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49 <when value="file">
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50 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
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51 </when>
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52 </conditional>
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53 </xml>
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54 <xml name="chromosomes">
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55 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
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56 <sanitizer invalid_char="">
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57 <valid initial="string.letters,string.digits">
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58 <add value="_" />
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59 <add value="." />
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60 <add value="," />
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61 </valid>
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62 </sanitizer>
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63 </param>
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64 </xml>
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65 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
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66 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
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67 </xml>
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68 <xml name="includes_genome">
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69 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
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70 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
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71 </xml>
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72 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file" token_checked="false">
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73 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
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74 </xml>
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75 <xml name="excludes_genome">
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76 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
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77 <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/>
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78 <expand macro="exclude" exclude_what="genomic-cds" exclude_label="Exclude cds from genomic sequence file"/>
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79 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
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80 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
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81 </xml>
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82 <xml name="excludes_gene">
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83 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
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84 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
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85 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
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86 </xml>
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87 <xml name="excludes_virus_protein">
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88 <yield/>
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89 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
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90 <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/>
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91 <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/>
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92 <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/>
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93 </xml>
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94 <xml name="excludes_virus_genome">
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95 <expand macro="excludes_virus_protein">
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96 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
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97 </expand>
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98 </xml>
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99 <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
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100 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
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101 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
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102 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
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103 <xml name="includes_virus_genome">
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104 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
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105 </xml>
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106 <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
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107 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
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108 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
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109 <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)"></param>
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110 </xml>
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111 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
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112 --released-before '$filters.released_before'
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113 #end if
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114 </token>
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115 <token name="@RELEASED_SINCE@">#if $filters.released_since:
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116 --released-since '$filters.released_since'
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117 #end if
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118 </token>
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119 </macros>