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comparison macros.xml @ 3:c87df3f9e19d 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 08:20:15 +0000
parents c6009f4d7261
children 41c18b994108
comparison
equal deleted inserted replaced
2:2753a5786114 3:c87df3f9e19d
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">11.25.1</token> 2 <token name="@TOOL_VERSION@">12.27.1</token>
3 <token name="@PROFILE@">20.01</token> 3 <token name="@PROFILE@">20.01</token>
4 <token name="@LICENSE@">MIT</token> 4 <token name="@LICENSE@">MIT</token>
5 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token> 5 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
6 <token name="@SETUP_CERTIFICATES@"><![CDATA[ 6 <token name="@SETUP_CERTIFICATES@"><![CDATA[
7 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates 7 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates
8 [ -f /usr/local/ssl/cacert.pem ] && export export SSL_CERT_FILE="/usr/local/ssl/cacert.pem"; 8 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
9 ]]></token> 9 ]]></token>
10 <xml name="requirements"> 10 <xml name="requirements">
11 <requirements> 11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
13 <requirement type="package" version="2021.5.30">ca-certificates</requirement> 13 <requirement type="package" version="2021.5.30">ca-certificates</requirement>
49 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/> 49 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
50 </when> 50 </when>
51 </conditional> 51 </conditional>
52 </xml> 52 </xml>
53 <xml name="chromosomes"> 53 <xml name="chromosomes">
54 <param argument="--chromosomes" type="text" value="all" label="Limit chromosomes to a comma-delimited list of chromosomes"> 54 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
55 <sanitizer invalid_char=""> 55 <sanitizer invalid_char="">
56 <valid initial="string.letters,string.digits"> 56 <valid initial="string.letters,string.digits">
57 <add value="_" /> 57 <add value="_" />
58 <add value="." /> 58 <add value="." />
59 <add value="," /> 59 <add value="," />
60 </valid> 60 </valid>
61 </sanitizer> 61 </sanitizer>
62 </param> 62 </param>
63 </xml> 63 </xml>
64 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
65 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
66 </xml>
67 <xml name="includes_genome">
68 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
69 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
70 </xml>
64 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file"> 71 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file">
65 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" /> 72 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" />
66 </xml> 73 </xml>
74 <xml name="anti-exclude" token_exclude_what="gff3" token_exclude_label="Include gff3 annotation file" token_checked="false">
75 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" falsevalue="--exclude-@EXCLUDE_WHAT@" truevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
76 </xml>
67 <xml name="excludes_genome"> 77 <xml name="excludes_genome">
68 <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/> 78 <expand macro="anti-exclude" exclude_what="seq" exclude_label="Include genomic sequence file" checked="true"/>
69 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/> 79 <expand macro="anti-exclude" exclude_what="gff3" exclude_label="Include gff3 annotation file"/>
70 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/> 80 <expand macro="anti-exclude" exclude_what="genomic-cds" exclude_label="Include cds from genomic sequence file"/>
71 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/> 81 <expand macro="anti-exclude" exclude_what="protein" exclude_label="Include protein sequence file"/>
82 <expand macro="anti-exclude" exclude_what="rna" exclude_label="Include transcript sequence file"/>
72 </xml> 83 </xml>
73 <xml name="excludes_gene"> 84 <xml name="excludes_gene">
74 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/> 85 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
75 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/> 86 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
76 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/> 87 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
85 <xml name="excludes_virus_genome"> 96 <xml name="excludes_virus_genome">
86 <expand macro="excludes_virus_protein"> 97 <expand macro="excludes_virus_protein">
87 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/> 98 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
88 </expand> 99 </expand>
89 </xml> 100 </xml>
90 <token name="@EXCLUDES_GENOME@">$exclude_gff3 $exclude_protein $exclude_rna $exclude_seq</token> 101 <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
91 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token> 102 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
92 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token> 103 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
93 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token> 104 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
94 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
95 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
96 </xml>
97 <xml name="includes_genome">
98 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
99 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
100 </xml>
101 <xml name="includes_virus_genome"> 105 <xml name="includes_virus_genome">
102 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/> 106 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
103 </xml> 107 </xml>
104 <token name="@INCLUDES_GENOME@">$include_gbff $include_gtf</token> 108 <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
105 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token> 109 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
106 <xml name="released_options" token_released_what="genomes" token_before_or_after="before"> 110 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
107 <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> 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>
108 </xml> 112 </xml>
109 <token name="@RELEASED_BEFORE@">#if $released_before: 113 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
110 --released-before '$released_before' 114 --released-before '$filters.released_before'
111 #end if 115 #end if
112 </token> 116 </token>
113 <token name="@RELEASED_SINCE@">#if $released_since: 117 <token name="@RELEASED_SINCE@">#if $filters.released_since:
114 --released-since '$released_since' 118 --released-since '$filters.released_since'
115 #end if 119 #end if
116 </token> 120 </token>
117 </macros> 121 </macros>