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comparison macros.xml @ 13:d979ba07ddd4 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 11:39:29 +0000
parents e8d51503c749
children a222b4d3d52e
comparison
equal deleted inserted replaced
12:e8d51503c749 13:d979ba07ddd4
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">13.35.0</token> 2 <token name="@TOOL_VERSION@">14.3</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.01</token> 4 <token name="@PROFILE@">21.01</token>
5 <token name="@LICENSE@">MIT</token> 5 <token name="@LICENSE@">MIT</token>
6 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token> 6 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
7 <token name="@SETUP_CERTIFICATES@"><![CDATA[ 7 <token name="@SETUP_CERTIFICATES@"><![CDATA[
9 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem"; 9 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
10 ]]></token> 10 ]]></token>
11 <xml name="requirements"> 11 <xml name="requirements">
12 <requirements> 12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
14 <requirement type="package" version="2022.6.15">ca-certificates</requirement> 14 <requirement type="package" version="2022.9.24">ca-certificates</requirement>
15 <requirement type="package" version="16.02">p7zip</requirement> 15 <requirement type="package" version="16.02">p7zip</requirement>
16 </requirements> 16 </requirements>
17 </xml> 17 </xml>
18 <xml name="annotation"> 18 <xml name="annotation">
19 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/> 19 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
20 </xml> 20 </xml>
21 <xml name="dehydrated">
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"/>
23 </xml>
24 <xml name="assembly_level"> 21 <xml name="assembly_level">
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"> 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">
26 <option value="chromosome">Chromosome</option> 23 <option value="chromosome">Chromosome</option>
27 <option value="complete_genome">Complete Genome</option> 24 <option value="complete">Complete Genome</option>
28 <option value="contig">Contig</option> 25 <option value="contig">Contig</option>
29 <option value="scaffold">Scaffold</option> 26 <option value="scaffold">Scaffold</option>
30 </param> 27 </param>
31 </xml> 28 </xml>
32 <xml name="assembly_source"> 29 <xml name="assembly_source">
33 <param argument="--assembly-source" type="select" optional="true"> 30 <param argument="--assembly-source" type="select" optional="true" label="Assembly source" help="Default (nothing selected) is both " >
34 <option value="refseq">RefSeq</option> 31 <option value="refseq">RefSeq</option>
35 <option value="genabnk">GenBank</option> 32 <option value="genbank">GenBank</option>
36 </param> 33 </param>
37 </xml> 34 </xml>
38 <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession"> 35 <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession">
39 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download"> 36 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
40 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?"> 37 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
60 <add value="," /> 57 <add value="," />
61 </valid> 58 </valid>
62 </sanitizer> 59 </sanitizer>
63 </param> 60 </param>
64 </xml> 61 </xml>
65 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available"> 62 <xml name="include">
66 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" /> 63 <param argument="--include" type="select" multiple="true" optional="true">
64 <option value="genome" selected="true">genomic sequence (genome)</option>
65 <option value="rna">transcript (rna)</option>
66 <option value="protein">amnio acid sequences (protein)</option>
67 <option value="cds">nucleotide coding sequences (cds)</option>
68 <option value="gff3">general feature file (gff3)</option>
69 <option value="gtf">gene transfer format (gtf)</option>
70 <option value="gbff">GenBank flat file (gbff)</option>
71 <option value="seq-report">sequence report file (seq-report)</option>
72 </param>
67 </xml> 73 </xml>
68 <xml name="includes_genome"> 74 <token name="@INCLUDE@"><![CDATA[
69 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/> 75 --include
70 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/> 76 #if $file_choices.include
71 </xml> 77 #echo ",".join($file_choices.include)
72 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file" token_checked="false"> 78 #else
73 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/> 79 none
74 </xml> 80 #end if
75 <xml name="excludes_genome"> 81 ]]></token>
76 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
77 <expand macro="exclude" exclude_what="gff3" exclude_label="Exclude gff3 annotation file"/>
78 <expand macro="exclude" exclude_what="genomic-cds" exclude_label="Exclude cds from genomic sequence file"/>
79 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
80 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
81 </xml>
82 <xml name="excludes_gene">
83 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
84 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
85 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
86 </xml>
87 <xml name="excludes_virus_protein">
88 <yield/>
89 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
90 <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/>
91 <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/>
92 <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/>
93 </xml>
94 <xml name="excludes_virus_genome">
95 <expand macro="excludes_virus_protein">
96 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
97 </expand>
98 </xml>
99 <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
100 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
101 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
102 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
103 <xml name="includes_virus_genome">
104 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
105 </xml>
106 <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
107 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
108 <xml name="released_options" token_released_what="genomes" token_before_or_after="before"> 82 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
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> 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)">
84 <validator type="regex" message="enter a date in the form MM/DD/YYYY">[0-9]{2}/[0-9]{2}/[0-9]{4}</validator>
85 </param>
110 </xml> 86 </xml>
111 <token name="@RELEASED_BEFORE@">#if $filters.released_before: 87 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
112 --released-before '$filters.released_before' 88 --released-before '$filters.released_before'
113 #end if 89 #end if
114 </token> 90 </token>
115 <token name="@RELEASED_SINCE@">#if $filters.released_since: 91 <token name="@RELEASED_AFTER@">#if $filters.released_after:
116 --released-since '$filters.released_since' 92 --released-after '$filters.released_after'
117 #end if 93 #end if
118 </token> 94 </token>
95
96 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1">
97 <element name="@EL1@">
98 <element name="@EL2@">
99 <assert_contents>
100 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/>
101 </assert_contents>
102 </element>
103 </element>
104 </xml>
119 </macros> 105 </macros>