Mercurial > repos > iuc > ncbi_datasets

annotate macros.xml @ 0:1a7773882d2c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
author iuc
date Thu, 27 Jan 2022 08:20:47 +0000
parents
children e34fcd410816
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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>
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2 <token name="@TOOL_VERSION@">12.27.1</token>
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3 <token name="@PROFILE@">20.01</token>
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4 <token name="@LICENSE@">MIT</token>
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5 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
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6 <token name="@SETUP_CERTIFICATES@"><![CDATA[
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7 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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8 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
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9 ]]></token>
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
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13 <requirement type="package" version="2021.5.30">ca-certificates</requirement>
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14 <requirement type="package" version="16.02">p7zip</requirement>
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15 </requirements>
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16 </xml>
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17 <xml name="annotation">
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18 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
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19 </xml>
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20 <xml name="dehydrated">
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21 <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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22 </xml>
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23 <xml name="assembly_level">
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24 <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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25 <option value="chromosome">Chromosome</option>
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26 <option value="complete_genome">Complete Genome</option>
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27 <option value="contig">Contig</option>
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28 <option value="scaffold">Scaffold</option>
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29 </param>
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30 </xml>
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31 <xml name="assembly_source">
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32 <param argument="--assembly-source" type="select" optional="true">
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33 <option value="refseq">RefSeq</option>
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34 <option value="genabnk">GenBank</option>
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35 </param>
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36 </xml>
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37 <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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38 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
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39 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
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40 <option value="text">Enter @WHAT@s</option>
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41 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
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42 </param>
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43 <when value="text">
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44 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@">
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45 <yield/>
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46 </param>
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47 </when>
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48 <when value="file">
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49 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
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50 </when>
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51 </conditional>
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52 </xml>
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53 <xml name="chromosomes">
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54 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
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55 <sanitizer invalid_char="">
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56 <valid initial="string.letters,string.digits">
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57 <add value="_" />
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58 <add value="." />
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59 <add value="," />
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 </xml>
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64 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
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65 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
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66 </xml>
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67 <xml name="includes_genome">
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68 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
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69 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
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70 </xml>
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71 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file">
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72 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" />
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73 </xml>
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74 <xml name="anti-exclude" token_exclude_what="gff3" token_exclude_label="Include gff3 annotation file" token_checked="false">
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75 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" falsevalue="--exclude-@EXCLUDE_WHAT@" truevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
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76 </xml>
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77 <xml name="excludes_genome">
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78 <expand macro="anti-exclude" exclude_what="seq" exclude_label="Include genomic sequence file" checked="true"/>
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79 <expand macro="anti-exclude" exclude_what="gff3" exclude_label="Include gff3 annotation file"/>
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80 <expand macro="anti-exclude" exclude_what="genomic-cds" exclude_label="Include cds from genomic sequence file"/>
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81 <expand macro="anti-exclude" exclude_what="protein" exclude_label="Include protein sequence file"/>
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82 <expand macro="anti-exclude" exclude_what="rna" exclude_label="Include transcript sequence file"/>
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83 </xml>
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84 <xml name="excludes_gene">
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85 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
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86 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
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87 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
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88 </xml>
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89 <xml name="excludes_virus_protein">
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90 <yield/>
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91 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
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92 <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/>
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93 <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/>
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94 <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/>
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95 </xml>
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96 <xml name="excludes_virus_genome">
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97 <expand macro="excludes_virus_protein">
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98 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
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99 </expand>
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100 </xml>
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101 <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
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102 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
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103 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
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104 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
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105 <xml name="includes_virus_genome">
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106 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
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107 </xml>
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108 <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
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109 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
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110 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
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111 <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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112 </xml>
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113 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
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114 --released-before '$filters.released_before'
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115 #end if
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116 </token>
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117 <token name="@RELEASED_SINCE@">#if $filters.released_since:
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118 --released-since '$filters.released_since'
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119 #end if
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120 </token>
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121 </macros>