Mercurial > repos > iuc > ncbi_datasets

annotate macros.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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1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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1 <macros>
10
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2 <token name="@TOOL_VERSION@">14.3</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>
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[
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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8 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates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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9 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
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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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a3395b1d871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3d012f702b54172f30a49543bf7e5fff2dd71f30
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14 <requirement type="package" version="2022.9.24">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="assembly_level">
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22 <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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23 <option value="chromosome">Chromosome</option>
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24 <option value="complete">Complete Genome</option>
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25 <option value="contig">Contig</option>
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26 <option value="scaffold">Scaffold</option>
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27 </param>
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28 </xml>
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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29 <xml name="assembly_source">
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30 <param argument="--assembly-source" type="select" optional="true" label="Assembly source" help="Default (nothing selected) is both " >
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31 <option value="refseq">RefSeq</option>
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32 <option value="genbank">GenBank</option>
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33 </param>
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34 </xml>
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35 <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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36 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
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37 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
1a7773882d2c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
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38 <option value="text">Enter @WHAT@s</option>
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39 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
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40 </param>
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41 <when value="text">
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42 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@">
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43 <yield/>
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44 </param>
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45 </when>
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46 <when value="file">
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47 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
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48 </when>
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49 </conditional>
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50 </xml>
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51 <xml name="chromosomes">
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52 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
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53 <sanitizer invalid_char="">
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54 <valid initial="string.letters,string.digits">
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55 <add value="_" />
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56 <add value="." />
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57 <add value="," />
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58 </valid>
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59 </sanitizer>
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60 </param>
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61 </xml>
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62 <xml name="include">
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63 <param argument="--include" type="select" multiple="true" optional="true">
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64 <option value="genome" selected="true">genomic sequence (genome)</option>
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65 <option value="rna">transcript (rna)</option>
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66 <option value="protein">amnio acid sequences (protein)</option>
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67 <option value="cds">nucleotide coding sequences (cds)</option>
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68 <option value="gff3">general feature file (gff3)</option>
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69 <option value="gtf">gene transfer format (gtf)</option>
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70 <option value="gbff">GenBank flat file (gbff)</option>
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71 <option value="seq-report">sequence report file (seq-report)</option>
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72 </param>
0
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73 </xml>
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74 <token name="@INCLUDE@"><![CDATA[
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75 --include
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76 #if $file_choices.include
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77 #echo ",".join($file_choices.include)
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78 #else
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79 none
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80 #end if
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81 ]]></token>
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82 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
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83 <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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84 <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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85 </param>
0
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86 </xml>
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87 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
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88 --released-before '$filters.released_before'
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89 #end if
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90 </token>
10
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91 <token name="@RELEASED_AFTER@">#if $filters.released_after:
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92 --released-after '$filters.released_after'
0
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93 #end if
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94 </token>
10
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95
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96 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1">
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97 <element name="@EL1@">
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98 <element name="@EL2@">
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99 <assert_contents>
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100 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/>
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101 </assert_contents>
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102 </element>
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103 </element>
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104 </xml>
0
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105 </macros>