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comparison macros.xml @ 14:a222b4d3d52e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9
author iuc
date Fri, 09 Dec 2022 15:11:04 +0000
parents d979ba07ddd4
children dfad868c911b
comparison
equal deleted inserted replaced
13:d979ba07ddd4 14:a222b4d3d52e
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">14.3</token> 2 <token name="@TOOL_VERSION@">14.6.0</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[
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="2022.9.24">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="bio_tools">
19 <xrefs>
20 <xref type="bio.tools">ncbi_datasets</xref>
21 </xrefs>
22 </xml>
23 <xml name="version_command"><![CDATA[
24 datasets --version | cut -d" " -f 3
25 ]]></xml>
18 <xml name="annotation"> 26 <xml name="annotation">
19 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/> 27 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
20 </xml> 28 </xml>
21 <xml name="assembly_level"> 29 <xml name="assembly_level">
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"> 30 <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true">
37 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?"> 45 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
38 <option value="text">Enter @WHAT@s</option> 46 <option value="text">Enter @WHAT@s</option>
39 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option> 47 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
40 </param> 48 </param>
41 <when value="text"> 49 <when value="text">
42 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@"> 50 <!-- command section also allows spaces as separator for backward compatibility
43 <yield/> 51 prefer comma because this is used also in other text params-->
52 <param name="accession" type="text" label="Enter comma separated list of @WHAT@s" help="@HELP@">
53 <validator type="length" min="1" message="Provide at least one @WHAT@"/>
44 </param> 54 </param>
45 </when> 55 </when>
46 <when value="file"> 56 <when value="file">
47 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/> 57 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
48 </when> 58 </when>
57 <add value="," /> 67 <add value="," />
58 </valid> 68 </valid>
59 </sanitizer> 69 </sanitizer>
60 </param> 70 </param>
61 </xml> 71 </xml>
72
73 <xml name="taxon_positional">
74 <param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."/>
75 </xml>
76
77 <xml name="ortholog">
78 <param argument="--ortholog" type="text" label="Retrieve orthologs for taxa" help="Retrieve data for an ortholog set. Provide one or more comma separated taxa (any rank) to filter results or 'all' for the complete set.">
79 <sanitizer invalid_char="">
80 <valid initial="string.letters,string.digits">
81 <add value=" " />
82 <add value="," />
83 <add value="-" />
84 </valid>
85 </sanitizer>
86 </param>
87 </xml>
88
62 <xml name="include"> 89 <xml name="include">
63 <param argument="--include" type="select" multiple="true" optional="true"> 90 <param argument="--include" type="select" multiple="true" optional="true" label="Include" help="Download the following datasets (if available)">
64 <option value="genome" selected="true">genomic sequence (genome)</option> 91 <yield/>
65 <option value="rna">transcript (rna)</option> 92 </param>
66 <option value="protein">amnio acid sequences (protein)</option> 93 </xml>
67 <option value="cds">nucleotide coding sequences (cds)</option> 94 <xml name="genome_includes">
68 <option value="gff3">general feature file (gff3)</option> 95 <option value="genome" selected="true">genomic sequence (genome)</option>
69 <option value="gtf">gene transfer format (gtf)</option> 96 <option value="rna">transcript (rna)</option>
70 <option value="gbff">GenBank flat file (gbff)</option> 97 <option value="protein">amnio acid sequences (protein)</option>
71 <option value="seq-report">sequence report file (seq-report)</option> 98 <option value="cds">nucleotide coding sequences (cds)</option>
72 </param> 99 <option value="gff3">general feature file (gff3)</option>
73 </xml> 100 <option value="gtf">gene transfer format (gtf)</option>
101 <option value="gbff">GenBank flat file (gbff)</option>
102 <option value="seq-report">sequence report file (seq-report)</option>
103 <yield/>
104 </xml>
105 <xml name="gene_includes">
106 <option value="gene">gene sequence (gene)</option>
107 <option value="protein" selected="true">amnio acid sequences (protein)</option>
108 <yield/>
109 </xml>
110
74 <token name="@INCLUDE@"><![CDATA[ 111 <token name="@INCLUDE@"><![CDATA[
75 --include 112 --include
76 #if $file_choices.include 113 #if $file_choices.include
77 #echo ",".join($file_choices.include) 114 #echo ",".join($file_choices.include)
78 #else 115 #else
79 none 116 none
80 #end if 117 #end if
81 ]]></token> 118 ]]></token>
119 <xml name="tsv_report_columns">
120 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
121 <option value="accession">Assembly Accession</option>
122 <option value="annotinfo-busco-complete">Annotation BUSCO Complete</option>
123 <option value="annotinfo-busco-duplicated">Annotation BUSCO Duplicated</option>
124 <option value="annotinfo-busco-fragmented">Annotation BUSCO Fragmented</option>
125 <option value="annotinfo-busco-lineage">Annotation BUSCO Lineage</option>
126 <option value="annotinfo-busco-missing">Annotation BUSCO Missing</option>
127 <option value="annotinfo-busco-singlecopy">Annotation BUSCO Single Copy</option>
128 <option value="annotinfo-busco-totalcount">Annotation BUSCO Total Count</option>
129 <option value="annotinfo-busco-ver">Annotation BUSCO Version</option>
130 <option value="annotinfo-featcount-gene-non-coding">Annotation Count Gene Non-coding</option>
131 <option value="annotinfo-featcount-gene-other">Annotation Count Gene Other</option>
132 <option value="annotinfo-featcount-gene-protein-coding">Annotation Count Gene Protein-coding</option>
133 <option value="annotinfo-featcount-gene-pseudogene">Annotation Count Gene Pseudogene</option>
134 <option value="annotinfo-featcount-gene-total">Annotation Count Gene Total</option>
135 <option value="annotinfo-method">Annotation Method</option>
136 <option value="annotinfo-name">Annotation Name</option>
137 <option value="annotinfo-pipeline">Annotation Pipeline</option>
138 <option value="annotinfo-provider">Annotation Provider</option>
139 <option value="annotinfo-release-date">Annotation Release Date</option>
140 <option value="annotinfo-release-version">Annotation Release Version</option>
141 <option value="annotinfo-report-url">Annotation Report URL</option>
142 <option value="annotinfo-software-version">Annotation Software Version</option>
143 <option value="annotinfo-status">Annotation Status</option>
144 <option value="assminfo-atypicalis-atypical">Assembly Atypical Is Atypical</option>
145 <option value="assminfo-atypicalwarnings">Assembly Atypical Warnings</option>
146 <option value="assminfo-bioproject-lineage-accession">Assembly BioProject Lineage Accession</option>
147 <option value="assminfo-bioproject-lineage-parent-accession">Assembly BioProject Lineage Parent Accession</option>
148 <option value="assminfo-bioproject-lineage-parent-accessions">Assembly BioProject Lineage Parent Accessions</option>
149 <option value="assminfo-bioproject-lineage-title">Assembly BioProject Lineage Title</option>
150 <option value="assminfo-biosample-accession">Assembly BioSample Accession</option>
151 <option value="assminfo-biosample-attribute-name">Assembly BioSample Attribute Name</option>
152 <option value="assminfo-biosample-attribute-value">Assembly BioSample Attribute Value</option>
153 <option value="assminfo-biosample-bioproject-accession">Assembly BioSample BioProject Accession</option>
154 <option value="assminfo-biosample-bioproject-parent-accession">Assembly BioSample BioProject Parent Accession</option>
155 <option value="assminfo-biosample-bioproject-parent-accessions">Assembly BioSample BioProject Parent Accessions</option>
156 <option value="assminfo-biosample-bioproject-title">Assembly BioSample BioProject Title</option>
157 <option value="assminfo-biosample-description-comment">Assembly BioSample Description Comment</option>
158 <option value="assminfo-biosample-description-organism-common-name">Assembly BioSample Description Organism Common Name</option>
159 <option value="assminfo-biosample-description-organism-infraspecific-breed">Assembly BioSample Description Organism Infraspecific Names Breed</option>
160 <option value="assminfo-biosample-description-organism-infraspecific-cultivar">Assembly BioSample Description Organism Infraspecific Names Cultivar</option>
161 <option value="assminfo-biosample-description-organism-infraspecific-ecotype">Assembly BioSample Description Organism Infraspecific Names Ecotype</option>
162 <option value="assminfo-biosample-description-organism-infraspecific-isolate">Assembly BioSample Description Organism Infraspecific Names Isolate</option>
163 <option value="assminfo-biosample-description-organism-infraspecific-sex">Assembly BioSample Description Organism Infraspecific Names Sex</option>
164 <option value="assminfo-biosample-description-organism-infraspecific-strain">Assembly BioSample Description Organism Infraspecific Names Strain</option>
165 <option value="assminfo-biosample-description-organism-name">Assembly BioSample Description Organism Name</option>
166 <option value="assminfo-biosample-description-organism-pangolin">Assembly BioSample Description Organism Pangolin Classification</option>
167 <option value="assminfo-biosample-description-organism-tax-id">Assembly BioSample Description Organism Taxonomic ID</option>
168 <option value="assminfo-biosample-description-title">Assembly BioSample Description Title</option>
169 <option value="assminfo-biosample-ids-db">Assembly BioSample Sample Identifiers Database</option>
170 <option value="assminfo-biosample-ids-label">Assembly BioSample Sample Identifiers Label</option>
171 <option value="assminfo-biosample-ids-value">Assembly BioSample Sample Identifiers Value</option>
172 <option value="assminfo-biosample-last-updated">Assembly BioSample Last updated</option>
173 <option value="assminfo-biosample-models">Assembly BioSample Models</option>
174 <option value="assminfo-biosample-owner-contact-lab">Assembly BioSample Owner Contact Lab</option>
175 <option value="assminfo-biosample-owner-name">Assembly BioSample Owner Name</option>
176 <option value="assminfo-biosample-package">Assembly BioSample Package</option>
177 <option value="assminfo-biosample-publication-date">Assembly BioSample Publication date</option>
178 <option value="assminfo-biosample-status-status">Assembly BioSample Status Status</option>
179 <option value="assminfo-biosample-status-when">Assembly BioSample Status When</option>
180 <option value="assminfo-biosample-submission-date">Assembly BioSample Submission date</option>
181 <option value="assminfo-blast-url">Assembly Blast URL</option>
182 <option value="assminfo-description">Assembly Description</option>
183 <option value="assminfo-level">Assembly Level</option>
184 <option value="assminfo-linked-assmaccession">Assembly Linked Assembly Accession</option>
185 <option value="assminfo-linked-assmtype">Assembly Linked Assembly Type</option>
186 <option value="assminfo-name">Assembly Name</option>
187 <option value="assminfo-paired-assmaccession">Assembly Paired Assembly Accession</option>
188 <option value="assminfo-paired-assmname">Assembly Paired Assembly Name</option>
189 <option value="assminfo-paired-assmstatus">Assembly Paired Assembly Status</option>
190 <option value="assminfo-refseq-category">Assembly Refseq Category</option>
191 <option value="assminfo-sequencing-tech">Assembly Sequencing Tech</option>
192 <option value="assminfo-status">Assembly Status</option>
193 <option value="assminfo-submission-date">Assembly Submission Date</option>
194 <option value="assminfo-submitter">Assembly Submitter</option>
195 <option value="assminfo-synonym">Assembly Synonym</option>
196 <option value="assminfo-type">Assembly Type</option>
197 <option value="assmstats-contig-l50">Assembly Stats Contig L50</option>
198 <option value="assmstats-contig-n50">Assembly Stats Contig N50</option>
199 <option value="assmstats-gaps-between-scaffolds-count">Assembly Stats Gaps Between Scaffolds Count</option>
200 <option value="assmstats-gc-count">Assembly Stats GC Count</option>
201 <option value="assmstats-gc-percent">Assembly Stats GC Percent</option>
202 <option value="assmstats-number-of-component-sequences">Assembly Stats Number of Component Sequences</option>
203 <option value="assmstats-number-of-contigs">Assembly Stats Number of Contigs</option>
204 <option value="assmstats-number-of-scaffolds">Assembly Stats Number of Scaffolds</option>
205 <option value="assmstats-scaffold-l50">Assembly Stats Scaffold L50</option>
206 <option value="assmstats-scaffold-n50">Assembly Stats Scaffold N50</option>
207 <option value="assmstats-total-number-of-chromosomes">Assembly Stats Total Number of Chromosomes</option>
208 <option value="assmstats-total-sequence-len">Assembly Stats Total Sequence Length</option>
209 <option value="assmstats-total-ungapped-len">Assembly Stats Total Ungapped Length</option>
210 <option value="current-accession">Current Accession</option>
211 <option value="organelle-assembly-name">Organelle Assembly Name</option>
212 <option value="organelle-bioproject-accessions">Organelle BioProject Accessions</option>
213 <option value="organelle-description">Organelle Description</option>
214 <option value="organelle-infraspecific-name">Organelle Infraspecific Name</option>
215 <option value="organelle-submitter">Organelle Submitter</option>
216 <option value="organelle-total-seq-length">Organelle Total Seq Length</option>
217 <option value="organism-common-name">Organism Common Name</option>
218 <option value="organism-infraspecific-breed">Organism Infraspecific Names Breed</option>
219 <option value="organism-infraspecific-cultivar">Organism Infraspecific Names Cultivar</option>
220 <option value="organism-infraspecific-ecotype">Organism Infraspecific Names Ecotype</option>
221 <option value="organism-infraspecific-isolate">Organism Infraspecific Names Isolate</option>
222 <option value="organism-infraspecific-sex">Organism Infraspecific Names Sex</option>
223 <option value="organism-infraspecific-strain">Organism Infraspecific Names Strain</option>
224 <option value="organism-name">Organism Name</option>
225 <option value="organism-pangolin">Organism Pangolin Classification</option>
226 <option value="organism-tax-id">Organism Taxonomic ID</option>
227 <option value="source_database">Source Database</option>
228 <option value="wgs-contigs-url">WGS contigs URL</option>
229 <option value="wgs-project-accession">WGS project accession</option>
230 <option value="wgs-url">WGS URL</option>
231 <yield/>
232 </param>
233 </xml>
234
235 <xml name="gene_tsv_report_columns">
236 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
237 <option value="annotation-assembly-accession">Annotation Assembly Accession</option>
238 <option value="annotation-assembly-name">Annotation Assembly Name</option>
239 <option value="annotation-genomic-range-accession">Annotation Genomic Range Accession</option>
240 <option value="annotation-genomic-range-exon-order">Annotation Genomic Range Exons Order</option>
241 <option value="annotation-genomic-range-exon-orientation">Annotation Genomic Range Exons Orientation</option>
242 <option value="annotation-genomic-range-exon-start">Annotation Genomic Range Exons Start</option>
243 <option value="annotation-genomic-range-exon-stop">Annotation Genomic Range Exons Stop</option>
244 <option value="annotation-genomic-range-range-order">Annotation Genomic Range Order</option>
245 <option value="annotation-genomic-range-range-orientation">Annotation Genomic Range Orientation</option>
246 <option value="annotation-genomic-range-range-start">Annotation Genomic Range Start</option>
247 <option value="annotation-genomic-range-range-stop">Annotation Genomic Range Stop</option>
248 <option value="annotation-genomic-range-seq-name">Annotation Genomic Range Seq Name</option>
249 <option value="annotation-release-date">Annotation Release Date</option>
250 <option value="annotation-release-name">Annotation Release Name</option>
251 <option value="chromosomes">Chromosomes</option>
252 <option value="common-name">Common Name</option>
253 <option value="description">Description</option>
254 <option value="ensembl-geneids">Ensembl GeneIDs</option>
255 <option value="gene-id">NCBI GeneID</option>
256 <option value="gene-type">Gene Type</option>
257 <option value="genomic-region-gene-range-accession">Genomic Region Gene Range Sequence Accession</option>
258 <option value="genomic-region-gene-range-range-order">Genomic Region Gene Range Order</option>
259 <option value="genomic-region-gene-range-range-orientation">Genomic Region Gene Range Orientation</option>
260 <option value="genomic-region-gene-range-range-start">Genomic Region Gene Range Start</option>
261 <option value="genomic-region-gene-range-range-stop">Genomic Region Gene Range Stop</option>
262 <option value="genomic-region-genomic-region-type">Genomic Region Genomic Region Type</option>
263 <option value="group-id">Gene Group Identifier</option>
264 <option value="group-method">Gene Group Method</option>
265 <option value="name-authority">Nomenclature Authority</option>
266 <option value="name-id">Nomenclature ID</option>
267 <option value="omim-ids">OMIM IDs</option>
268 <option value="orientation">Orientation</option>
269 <option value="ref-standard-gene-range-accession">Reference Standard Gene Range Sequence Accession</option>
270 <option value="ref-standard-gene-range-range-order">Reference Standard Gene Range Order</option>
271 <option value="ref-standard-gene-range-range-orientation">Reference Standard Gene Range Orientation</option>
272 <option value="ref-standard-gene-range-range-start">Reference Standard Gene Range Start</option>
273 <option value="ref-standard-gene-range-range-stop">Reference Standard Gene Range Stop</option>
274 <option value="ref-standard-genomic-region-type">Reference Standard Genomic Region Type</option>
275 <option value="replaced-gene-id">Replaced NCBI GeneID</option>
276 <option value="rna-type">RNA Type</option>
277 <option value="swissprot-accessions">SwissProt Accessions</option>
278 <option value="symbol">Symbol</option>
279 <option value="synonyms">Synonyms</option>
280 <option value="tax-id">Taxonomic ID</option>
281 <option value="tax-name">Taxonomic Name</option>
282 <yield/>
283 </param>
284 </xml>
285 <xml name="prok_gene_tsv_report_columns">
286 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report">
287 <option value="accession">Accession</option>
288 <option value="description">Description</option>
289 <option value="ec-number">EC Number</option>
290 <option value="gene-symbol">Gene Symbol</option>
291 <option value="mapping-count">Number of Genome Mappings</option>
292 <option value="name-evidence-accession">Protein Name EvidenceAccession</option>
293 <option value="name-evidence-category">Protein Name EvidenceCategory</option>
294 <option value="name-evidence-source">Protein Name EvidenceSource</option>
295 <option value="protein-length">Protein Length</option>
296 <option value="protein-name">Protein Name</option>
297 <yield/>
298 </param>
299 </xml>
82 <xml name="released_options" token_released_what="genomes" token_before_or_after="before"> 300 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
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)"> 301 <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> 302 <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> 303 </param>
86 </xml> 304 </xml>
90 </token> 308 </token>
91 <token name="@RELEASED_AFTER@">#if $filters.released_after: 309 <token name="@RELEASED_AFTER@">#if $filters.released_after:
92 --released-after '$filters.released_after' 310 --released-after '$filters.released_after'
93 #end if 311 #end if
94 </token> 312 </token>
95 313 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_ftype="fasta" token_expression_n="1">
96 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1">
97 <element name="@EL1@"> 314 <element name="@EL1@">
98 <element name="@EL2@"> 315 <element name="@EL2@" ftype="@FTYPE@" decompress="true">
99 <assert_contents> 316 <assert_contents>
100 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/> 317 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/>
101 </assert_contents> 318 </assert_contents>
102 </element> 319 </element>
103 </element> 320 </element>
104 </xml> 321 </xml>
322 <xml name="citations">
323 <citations>
324 <citation type="bibtex">@misc{NCBI,
325 author = "{NCBI}",
326 title = "NCBI Datasets",
327 year = "2022",
328 url = "https://github.com/ncbi/datasets"}
329 </citation>
330 </citations>
331 </xml>
105 </macros> 332 </macros>