Mercurial > repos > iuc > ncbi_datasets
comparison macros.xml @ 11:ac24fff14f23 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 4d7d3a56084e140f4fa63fb0e04a08b732f247f2
author | iuc |
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date | Fri, 02 Dec 2022 10:52:48 +0000 |
parents | a3395b1d871b |
children | d78faac2c6ef |
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10:a3395b1d871b | 11:ac24fff14f23 |
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1 <macros> | 1 <macros> |
2 <token name="@TOOL_VERSION@">14.3</token> | 2 <token name="@TOOL_VERSION@">14.4</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[ |
37 <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 ?"> |
38 <option value="text">Enter @WHAT@s</option> | 38 <option value="text">Enter @WHAT@s</option> |
39 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option> | 39 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option> |
40 </param> | 40 </param> |
41 <when value="text"> | 41 <when value="text"> |
42 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@"> | 42 <!-- command section also allows spaces as separator for backward compatibility |
43 <yield/> | 43 prefer comma because this is used also in other text params--> |
44 <param name="accession" type="text" label="Enter comma separated list of @WHAT@s" help="@HELP@"> | |
45 <validator type="length" min="1" message="Provide at least one @WHAT@"/> | |
44 </param> | 46 </param> |
45 </when> | 47 </when> |
46 <when value="file"> | 48 <when value="file"> |
47 <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@"/> |
48 </when> | 50 </when> |
57 <add value="," /> | 59 <add value="," /> |
58 </valid> | 60 </valid> |
59 </sanitizer> | 61 </sanitizer> |
60 </param> | 62 </param> |
61 </xml> | 63 </xml> |
64 | |
65 <xml name="taxon_positional"> | |
66 <param name="taxon_positional" type="text" label="Enter taxon" help="e.g. human, mouse, bos taurus, etc."/> | |
67 </xml> | |
68 | |
69 <xml name="ortholog"> | |
70 <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."> | |
71 <sanitizer invalid_char=""> | |
72 <valid initial="string.letters,string.digits"> | |
73 <add value=" " /> | |
74 <add value="," /> | |
75 <add value="-" /> | |
76 </valid> | |
77 </sanitizer> | |
78 </param> | |
79 </xml> | |
80 | |
62 <xml name="include"> | 81 <xml name="include"> |
63 <param argument="--include" type="select" multiple="true" optional="true"> | 82 <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> | 83 <yield/> |
65 <option value="rna">transcript (rna)</option> | 84 </param> |
66 <option value="protein">amnio acid sequences (protein)</option> | 85 </xml> |
67 <option value="cds">nucleotide coding sequences (cds)</option> | 86 <xml name="genome_includes"> |
68 <option value="gff3">general feature file (gff3)</option> | 87 <option value="genome" selected="true">genomic sequence (genome)</option> |
69 <option value="gtf">gene transfer format (gtf)</option> | 88 <option value="rna">transcript (rna)</option> |
70 <option value="gbff">GenBank flat file (gbff)</option> | 89 <option value="protein">amnio acid sequences (protein)</option> |
71 <option value="seq-report">sequence report file (seq-report)</option> | 90 <option value="cds">nucleotide coding sequences (cds)</option> |
72 </param> | 91 <option value="gff3">general feature file (gff3)</option> |
73 </xml> | 92 <option value="gtf">gene transfer format (gtf)</option> |
93 <option value="gbff">GenBank flat file (gbff)</option> | |
94 <option value="seq-report">sequence report file (seq-report)</option> | |
95 <yield/> | |
96 </xml> | |
97 <xml name="gene_includes"> | |
98 <option value="gene">gene sequence (gene)</option> | |
99 <option value="protein" selected="true">amnio acid sequences (protein)</option> | |
100 <yield/> | |
101 </xml> | |
102 | |
74 <token name="@INCLUDE@"><![CDATA[ | 103 <token name="@INCLUDE@"><![CDATA[ |
75 --include | 104 --include |
76 #if $file_choices.include | 105 #if $file_choices.include |
77 #echo ",".join($file_choices.include) | 106 #echo ",".join($file_choices.include) |
78 #else | 107 #else |
79 none | 108 none |
80 #end if | 109 #end if |
81 ]]></token> | 110 ]]></token> |
111 <xml name="tsv_report_columns"> | |
112 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report"> | |
113 <option value="accession">Assembly Accession</option> | |
114 <option value="annotinfo-busco-complete">Annotation BUSCO Complete</option> | |
115 <option value="annotinfo-busco-duplicated">Annotation BUSCO Duplicated</option> | |
116 <option value="annotinfo-busco-fragmented">Annotation BUSCO Fragmented</option> | |
117 <option value="annotinfo-busco-lineage">Annotation BUSCO Lineage</option> | |
118 <option value="annotinfo-busco-missing">Annotation BUSCO Missing</option> | |
119 <option value="annotinfo-busco-singlecopy">Annotation BUSCO Single Copy</option> | |
120 <option value="annotinfo-busco-totalcount">Annotation BUSCO Total Count</option> | |
121 <option value="annotinfo-busco-ver">Annotation BUSCO Version</option> | |
122 <option value="annotinfo-featcount-gene-non-coding">Annotation Count Gene Non-coding</option> | |
123 <option value="annotinfo-featcount-gene-other">Annotation Count Gene Other</option> | |
124 <option value="annotinfo-featcount-gene-protein-coding">Annotation Count Gene Protein-coding</option> | |
125 <option value="annotinfo-featcount-gene-pseudogene">Annotation Count Gene Pseudogene</option> | |
126 <option value="annotinfo-featcount-gene-total">Annotation Count Gene Total</option> | |
127 <option value="annotinfo-method">Annotation Method</option> | |
128 <option value="annotinfo-name">Annotation Name</option> | |
129 <option value="annotinfo-pipeline">Annotation Pipeline</option> | |
130 <option value="annotinfo-provider">Annotation Provider</option> | |
131 <option value="annotinfo-release-date">Annotation Release Date</option> | |
132 <option value="annotinfo-release-version">Annotation Release Version</option> | |
133 <option value="annotinfo-report-url">Annotation Report URL</option> | |
134 <option value="annotinfo-software-version">Annotation Software Version</option> | |
135 <option value="annotinfo-status">Annotation Status</option> | |
136 <option value="assminfo-atypicalis-atypical">Assembly Atypical Is Atypical</option> | |
137 <option value="assminfo-atypicalwarnings">Assembly Atypical Warnings</option> | |
138 <option value="assminfo-bioproject-lineage-accession">Assembly BioProject Lineage Accession</option> | |
139 <option value="assminfo-bioproject-lineage-parent-accession">Assembly BioProject Lineage Parent Accession</option> | |
140 <option value="assminfo-bioproject-lineage-parent-accessions">Assembly BioProject Lineage Parent Accessions</option> | |
141 <option value="assminfo-bioproject-lineage-title">Assembly BioProject Lineage Title</option> | |
142 <option value="assminfo-biosample-accession">Assembly BioSample Accession</option> | |
143 <option value="assminfo-biosample-attribute-name">Assembly BioSample Attribute Name</option> | |
144 <option value="assminfo-biosample-attribute-value">Assembly BioSample Attribute Value</option> | |
145 <option value="assminfo-biosample-bioproject-accession">Assembly BioSample BioProject Accession</option> | |
146 <option value="assminfo-biosample-bioproject-parent-accession">Assembly BioSample BioProject Parent Accession</option> | |
147 <option value="assminfo-biosample-bioproject-parent-accessions">Assembly BioSample BioProject Parent Accessions</option> | |
148 <option value="assminfo-biosample-bioproject-title">Assembly BioSample BioProject Title</option> | |
149 <option value="assminfo-biosample-description-comment">Assembly BioSample Description Comment</option> | |
150 <option value="assminfo-biosample-description-organism-common-name">Assembly BioSample Description Organism Common Name</option> | |
151 <option value="assminfo-biosample-description-organism-infraspecific-breed">Assembly BioSample Description Organism Infraspecific Names Breed</option> | |
152 <option value="assminfo-biosample-description-organism-infraspecific-cultivar">Assembly BioSample Description Organism Infraspecific Names Cultivar</option> | |
153 <option value="assminfo-biosample-description-organism-infraspecific-ecotype">Assembly BioSample Description Organism Infraspecific Names Ecotype</option> | |
154 <option value="assminfo-biosample-description-organism-infraspecific-isolate">Assembly BioSample Description Organism Infraspecific Names Isolate</option> | |
155 <option value="assminfo-biosample-description-organism-infraspecific-sex">Assembly BioSample Description Organism Infraspecific Names Sex</option> | |
156 <option value="assminfo-biosample-description-organism-infraspecific-strain">Assembly BioSample Description Organism Infraspecific Names Strain</option> | |
157 <option value="assminfo-biosample-description-organism-name">Assembly BioSample Description Organism Name</option> | |
158 <option value="assminfo-biosample-description-organism-pangolin">Assembly BioSample Description Organism Pangolin Classification</option> | |
159 <option value="assminfo-biosample-description-organism-tax-id">Assembly BioSample Description Organism Taxonomic ID</option> | |
160 <option value="assminfo-biosample-description-title">Assembly BioSample Description Title</option> | |
161 <option value="assminfo-biosample-ids-db">Assembly BioSample Sample Identifiers Database</option> | |
162 <option value="assminfo-biosample-ids-label">Assembly BioSample Sample Identifiers Label</option> | |
163 <option value="assminfo-biosample-ids-value">Assembly BioSample Sample Identifiers Value</option> | |
164 <option value="assminfo-biosample-last-updated">Assembly BioSample Last updated</option> | |
165 <option value="assminfo-biosample-models">Assembly BioSample Models</option> | |
166 <option value="assminfo-biosample-owner-contact-lab">Assembly BioSample Owner Contact Lab</option> | |
167 <option value="assminfo-biosample-owner-name">Assembly BioSample Owner Name</option> | |
168 <option value="assminfo-biosample-package">Assembly BioSample Package</option> | |
169 <option value="assminfo-biosample-publication-date">Assembly BioSample Publication date</option> | |
170 <option value="assminfo-biosample-status-status">Assembly BioSample Status Status</option> | |
171 <option value="assminfo-biosample-status-when">Assembly BioSample Status When</option> | |
172 <option value="assminfo-biosample-submission-date">Assembly BioSample Submission date</option> | |
173 <option value="assminfo-blast-url">Assembly Blast URL</option> | |
174 <option value="assminfo-description">Assembly Description</option> | |
175 <option value="assminfo-level">Assembly Level</option> | |
176 <option value="assminfo-linked-assmaccession">Assembly Linked Assembly Accession</option> | |
177 <option value="assminfo-linked-assmtype">Assembly Linked Assembly Type</option> | |
178 <option value="assminfo-name">Assembly Name</option> | |
179 <option value="assminfo-paired-assmaccession">Assembly Paired Assembly Accession</option> | |
180 <option value="assminfo-paired-assmname">Assembly Paired Assembly Name</option> | |
181 <option value="assminfo-paired-assmstatus">Assembly Paired Assembly Status</option> | |
182 <option value="assminfo-refseq-category">Assembly Refseq Category</option> | |
183 <option value="assminfo-sequencing-tech">Assembly Sequencing Tech</option> | |
184 <option value="assminfo-status">Assembly Status</option> | |
185 <option value="assminfo-submission-date">Assembly Submission Date</option> | |
186 <option value="assminfo-submitter">Assembly Submitter</option> | |
187 <option value="assminfo-synonym">Assembly Synonym</option> | |
188 <option value="assminfo-type">Assembly Type</option> | |
189 <option value="assmstats-contig-l50">Assembly Stats Contig L50</option> | |
190 <option value="assmstats-contig-n50">Assembly Stats Contig N50</option> | |
191 <option value="assmstats-gaps-between-scaffolds-count">Assembly Stats Gaps Between Scaffolds Count</option> | |
192 <option value="assmstats-gc-count">Assembly Stats GC Count</option> | |
193 <option value="assmstats-gc-percent">Assembly Stats GC Percent</option> | |
194 <option value="assmstats-number-of-component-sequences">Assembly Stats Number of Component Sequences</option> | |
195 <option value="assmstats-number-of-contigs">Assembly Stats Number of Contigs</option> | |
196 <option value="assmstats-number-of-scaffolds">Assembly Stats Number of Scaffolds</option> | |
197 <option value="assmstats-scaffold-l50">Assembly Stats Scaffold L50</option> | |
198 <option value="assmstats-scaffold-n50">Assembly Stats Scaffold N50</option> | |
199 <option value="assmstats-total-number-of-chromosomes">Assembly Stats Total Number of Chromosomes</option> | |
200 <option value="assmstats-total-sequence-len">Assembly Stats Total Sequence Length</option> | |
201 <option value="assmstats-total-ungapped-len">Assembly Stats Total Ungapped Length</option> | |
202 <option value="current-accession">Current Accession</option> | |
203 <option value="organelle-assembly-name">Organelle Assembly Name</option> | |
204 <option value="organelle-bioproject-accessions">Organelle BioProject Accessions</option> | |
205 <option value="organelle-description">Organelle Description</option> | |
206 <option value="organelle-infraspecific-name">Organelle Infraspecific Name</option> | |
207 <option value="organelle-submitter">Organelle Submitter</option> | |
208 <option value="organelle-total-seq-length">Organelle Total Seq Length</option> | |
209 <option value="organism-common-name">Organism Common Name</option> | |
210 <option value="organism-infraspecific-breed">Organism Infraspecific Names Breed</option> | |
211 <option value="organism-infraspecific-cultivar">Organism Infraspecific Names Cultivar</option> | |
212 <option value="organism-infraspecific-ecotype">Organism Infraspecific Names Ecotype</option> | |
213 <option value="organism-infraspecific-isolate">Organism Infraspecific Names Isolate</option> | |
214 <option value="organism-infraspecific-sex">Organism Infraspecific Names Sex</option> | |
215 <option value="organism-infraspecific-strain">Organism Infraspecific Names Strain</option> | |
216 <option value="organism-name">Organism Name</option> | |
217 <option value="organism-pangolin">Organism Pangolin Classification</option> | |
218 <option value="organism-tax-id">Organism Taxonomic ID</option> | |
219 <option value="source_database">Source Database</option> | |
220 <option value="wgs-contigs-url">WGS contigs URL</option> | |
221 <option value="wgs-project-accession">WGS project accession</option> | |
222 <option value="wgs-url">WGS URL</option> | |
223 <yield/> | |
224 </param> | |
225 </xml> | |
226 | |
227 <xml name="gene_tsv_report_columns"> | |
228 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report"> | |
229 <option value="annotation-assembly-accession">Annotation Assembly Accession</option> | |
230 <option value="annotation-assembly-name">Annotation Assembly Name</option> | |
231 <option value="annotation-genomic-range-accession">Annotation Genomic Range Accession</option> | |
232 <option value="annotation-genomic-range-exon-order">Annotation Genomic Range Exons Order</option> | |
233 <option value="annotation-genomic-range-exon-orientation">Annotation Genomic Range Exons Orientation</option> | |
234 <option value="annotation-genomic-range-exon-start">Annotation Genomic Range Exons Start</option> | |
235 <option value="annotation-genomic-range-exon-stop">Annotation Genomic Range Exons Stop</option> | |
236 <option value="annotation-genomic-range-range-order">Annotation Genomic Range Order</option> | |
237 <option value="annotation-genomic-range-range-orientation">Annotation Genomic Range Orientation</option> | |
238 <option value="annotation-genomic-range-range-start">Annotation Genomic Range Start</option> | |
239 <option value="annotation-genomic-range-range-stop">Annotation Genomic Range Stop</option> | |
240 <option value="annotation-genomic-range-seq-name">Annotation Genomic Range Seq Name</option> | |
241 <option value="annotation-release-date">Annotation Release Date</option> | |
242 <option value="annotation-release-name">Annotation Release Name</option> | |
243 <option value="chromosomes">Chromosomes</option> | |
244 <option value="common-name">Common Name</option> | |
245 <option value="description">Description</option> | |
246 <option value="ensembl-geneids">Ensembl GeneIDs</option> | |
247 <option value="gene-id">NCBI GeneID</option> | |
248 <option value="gene-type">Gene Type</option> | |
249 <option value="genomic-region-gene-range-accession">Genomic Region Gene Range Sequence Accession</option> | |
250 <option value="genomic-region-gene-range-range-order">Genomic Region Gene Range Order</option> | |
251 <option value="genomic-region-gene-range-range-orientation">Genomic Region Gene Range Orientation</option> | |
252 <option value="genomic-region-gene-range-range-start">Genomic Region Gene Range Start</option> | |
253 <option value="genomic-region-gene-range-range-stop">Genomic Region Gene Range Stop</option> | |
254 <option value="genomic-region-genomic-region-type">Genomic Region Genomic Region Type</option> | |
255 <option value="group-id">Gene Group Identifier</option> | |
256 <option value="group-method">Gene Group Method</option> | |
257 <option value="name-authority">Nomenclature Authority</option> | |
258 <option value="name-id">Nomenclature ID</option> | |
259 <option value="omim-ids">OMIM IDs</option> | |
260 <option value="orientation">Orientation</option> | |
261 <option value="ref-standard-gene-range-accession">Reference Standard Gene Range Sequence Accession</option> | |
262 <option value="ref-standard-gene-range-range-order">Reference Standard Gene Range Order</option> | |
263 <option value="ref-standard-gene-range-range-orientation">Reference Standard Gene Range Orientation</option> | |
264 <option value="ref-standard-gene-range-range-start">Reference Standard Gene Range Start</option> | |
265 <option value="ref-standard-gene-range-range-stop">Reference Standard Gene Range Stop</option> | |
266 <option value="ref-standard-genomic-region-type">Reference Standard Genomic Region Type</option> | |
267 <option value="replaced-gene-id">Replaced NCBI GeneID</option> | |
268 <option value="rna-type">RNA Type</option> | |
269 <option value="swissprot-accessions">SwissProt Accessions</option> | |
270 <option value="symbol">Symbol</option> | |
271 <option value="synonyms">Synonyms</option> | |
272 <option value="tax-id">Taxonomic ID</option> | |
273 <option value="tax-name">Taxonomic Name</option> | |
274 <yield/> | |
275 </param> | |
276 </xml> | |
277 <xml name="prok_gene_tsv_report_columns"> | |
278 <param name="report_columns" type="select" multiple="true" optional="false" label="Columns in the report"> | |
279 <option value="accession">Accession</option> | |
280 <option value="description">Description</option> | |
281 <option value="ec-number">EC Number</option> | |
282 <option value="gene-symbol">Gene Symbol</option> | |
283 <option value="mapping-count">Number of Genome Mappings</option> | |
284 <option value="name-evidence-accession">Protein Name EvidenceAccession</option> | |
285 <option value="name-evidence-category">Protein Name EvidenceCategory</option> | |
286 <option value="name-evidence-source">Protein Name EvidenceSource</option> | |
287 <option value="protein-length">Protein Length</option> | |
288 <option value="protein-name">Protein Name</option> | |
289 <yield/> | |
290 </param> | |
291 </xml> | |
82 <xml name="released_options" token_released_what="genomes" token_before_or_after="before"> | 292 <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)"> | 293 <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> | 294 <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> | 295 </param> |
86 </xml> | 296 </xml> |
91 <token name="@RELEASED_AFTER@">#if $filters.released_after: | 301 <token name="@RELEASED_AFTER@">#if $filters.released_after: |
92 --released-after '$filters.released_after' | 302 --released-after '$filters.released_after' |
93 #end if | 303 #end if |
94 </token> | 304 </token> |
95 | 305 |
96 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_expression_n="1"> | 306 <xml name="genome_fasta_assert" tokens="el1,el2,expression" token_ftype="fasta" token_expression_n="1"> |
97 <element name="@EL1@"> | 307 <element name="@EL1@"> |
98 <element name="@EL2@"> | 308 <element name="@EL2@" ftype="@FTYPE@" decompress="true"> |
99 <assert_contents> | 309 <assert_contents> |
100 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/> | 310 <has_text_matching expression="@EXPRESSION@" n="@EXPRESSION_N@"/> |
101 </assert_contents> | 311 </assert_contents> |
102 </element> | 312 </element> |
103 </element> | 313 </element> |