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comparison samples_macros.xml @ 10:480d9e9d156b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
author iuc
date Fri, 27 Oct 2023 19:44:40 +0000
parents 6f6537780379
children f803a68fc9e5
comparison
equal deleted inserted replaced
9:a62c4a11a67d 10:480d9e9d156b
42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option> 42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option>
43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option> 43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option>
44 </param> 44 </param>
45 </xml> 45 </xml>
46 <xml name="test_submit_section"> 46 <xml name="test_submit_section">
47 <section name="test_submit_parameters" expanded="true" title="Testing options"> 47 <section name="test_submit_parameters" expanded="True" title="Testing options">
48 <param name="submit_dev" type="boolean" truevalue="true" falsevalue="false" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" /> 48 <param name="submit_dev" type="boolean" truevalue="True" falsevalue="False" label="Submit to test ENA server?" help="By selecting yes the reads will be submitted to the ENA test server. Uploads to test platform will not be public and will be removed in 24hrs. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find the uploads to the test platform at https://wwwdev.ebi.ac.uk/ena/" />
49 <param name="dry_run" type="boolean" truevalue="true" falsevalue="false" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/> 49 <param name="dry_run" type="boolean" truevalue="True" falsevalue="False" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
50 </section> 50 </section>
51 </xml> 51 </xml>
52 <xml name="run_inputs_macro"> 52 <xml name="run_inputs_macro">
53 <conditional name="run_input_format_conditional"> 53 <conditional name="run_input_format_conditional">
54 <param name="run_input_format" type="select" label="Select runs input format"> 54 <param name="run_input_format" type="select" label="Select runs input format">
55 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> 55 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
56 <option value="paired_list" selected="False">Input from a paired collection</option> 56 <option value="paired_list" selected="False">Input from a paired collection</option>
57 </param> 57 </param>
58 <when value="multiple_selection_list"> 58 <when value="multiple_selection_list">
59 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/> 59 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz,.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
60 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/> 60 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select individual datasets or a dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
61 </when> 61 </when>
62 <when value="paired_list"> 62 <when value="paired_list">
63 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" /> 63 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" label="List of paired-end runs files" help="Names should match the compressed run's files names defined in the metadata" />
64 </when> 64 </when>
65 </conditional> 65 </conditional>
66 </xml> 66 </xml>
67 <xml name="table_inputs_macro"> 67 <xml name="table_inputs_macro">
68 <conditional name="input_format_conditional"> 68 <conditional name="input_format_conditional">
69 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> 69 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option> 70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option>
71 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> 71 <option value="build_tables" selected="False">Interactive generation of the study structure (only recommended for small studies)</option>
72 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> 72 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
73 </param> 73 </param>
74 <when value="excel_tables"> 74 <when value="excel_tables">
75 <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />--> 75 <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
76 <expand macro="checklist_input_macro"/> 76 <expand macro="checklist_input_macro"/>
79 </when> 79 </when>
80 <when value="user_generated_tables"> 80 <when value="user_generated_tables">
81 <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />--> 81 <!--<param name="viral_submission" type="boolean" label="Does your submission data belong to a viral sample?" help="If you select yes then your data will be submitted using the ENA virus pathogen reporting standard checklist (see: https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html)" />-->
82 <expand macro="checklist_input_macro"/> 82 <expand macro="checklist_input_macro"/>
83 <expand macro="run_inputs_macro" /> 83 <expand macro="run_inputs_macro" />
84 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> 84 <param name="studies_users_table" type="data" format="tabular" multiple="False" label="Studies table" help="Studies metadata file"/>
85 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> 85 <param name="samples_users_table" type="data" format="tabular" multiple="False" label="Samples table" help="Samples metadata file"/>
86 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> 86 <param name="experiments_users_table" type="data" format="tabular" multiple="False" label="Experiments table" help="Experiments metadata file"/>
87 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> 87 <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/>
88 </when> 88 </when>
89 <when value="build_tables"> 89 <when value="build_tables">
90 <param name="add_extension" type="boolean" checked="false" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/> 90 <param name="add_extension" type="boolean" checked="False" label="Add .fastq.(gz.bz2) extension to the Galaxy dataset names to match the ones described in the input tables?"/>
91 <conditional name="conditional_viral_metadata"> 91 <conditional name="conditional_viral_metadata">
92 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" /> 92 <param name="viral_sample" type="select" label="Select your sample type" help="Non-viral interactive submissions lack specific sample checklist attributes and are suboptimal. It's highly recommended to use Excel or TSV templates as input for a more comprehensive submission.">
93 <when value="true"> 93 <option value="True" selected="True">Viral</option>
94 <option value="False" selected="False">Non viral</option>
95 </param>
96 <when value="True">
94 <expand macro="viral_samples" /> 97 <expand macro="viral_samples" />
95 </when> 98 </when>
96 <when value="false"> 99 <when value="False">
97 <expand macro="nonviral_samples" /> 100 <expand macro="nonviral_samples" />
98 </when> 101 </when>
99 </conditional> 102 </conditional>
100 </when> 103 </when>
101 </conditional> 104 </conditional>
104 <xml name="viral_samples"> 107 <xml name="viral_samples">
105 <repeat name="rep_study" title="Study" min="1"> 108 <repeat name="rep_study" title="Study" min="1">
106 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> 109 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
107 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> 110 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
108 <param name="study_type" type="select" label="Please select the type of study"> 111 <param name="study_type" type="select" label="Please select the type of study">
109 <options from_data_table="study_type"> 112 <options from_data_table="study_type">
110 <column name="value" index="0"/> 113 <column name="value" index="0"/>
111 </options> 114 </options>
112 </param> 115 </param>
113 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> 116 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
114 <repeat name="rep_sample" title="Samples associated with this study" min="1" > 117 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
115 <param name="sample_title" type="text" label="Sample title"/> 118 <param name="sample_title" type="text" label="Sample title"/>
116 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> 119 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
144 <param name="collecting_institution" type="text" label="Collecting institution"/> 147 <param name="collecting_institution" type="text" label="Collecting institution"/>
145 <param name="isolate" type="text" label="Isolate"/> 148 <param name="isolate" type="text" label="Isolate"/>
146 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > 149 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
147 <param name="experiment_title" type="text" label="Specify an experiment title" /> 150 <param name="experiment_title" type="text" label="Specify an experiment title" />
148 <param name="experiment_design" type="text" label="Describe the experiment design" /> 151 <param name="experiment_design" type="text" label="Describe the experiment design" />
149 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library"> 152 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
150 <options from_data_table="library_strategy"> 153 <options from_data_table="library_strategy">
151 <column name="value" index="0"/> 154 <column name="value" index="0"/>
152 </options> 155 </options>
153 </param> 156 </param>
154 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced"> 157 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
155 <options from_data_table="library_source"> 158 <options from_data_table="library_source">
156 <column name="value" index="0"/> 159 <column name="value" index="0"/>
157 </options> 160 </options>
158 </param> 161 </param>
159 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced"> 162 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
160 <options from_data_table="library_selection"> 163 <options from_data_table="library_selection">
161 <column name="value" index="0"/> 164 <column name="value" index="0"/>
162 </options> 165 </options>
163 </param> 166 </param>
164 <param name="library_layout" type="select" label="Library layout"> 167 <param name="library_layout" type="select" label="Library layout">
167 </options> 170 </options>
168 </param> 171 </param>
169 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> 172 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
170 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> 173 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
171 <param name="platform" type="select" label="Select the sequencing platform used"> 174 <param name="platform" type="select" label="Select the sequencing platform used">
172 <option value="LS454">LS454</option> 175 <options from_data_table="platform">
173 <option value="ILLUMINA">Illumina</option> 176 <column name="value" index="0"/>
174 <option value="HELICOS">Helicos</option> 177 </options>
175 <option value="ABI_SOLID">ABI Solid</option>
176 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
177 <option value="BGISEQ">BGI Seq</option>
178 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
179 <option value="PACBIO_SMRT">PacBio</option>
180 <option value="ION_TORRENT">Ion Torrent</option>
181 <option value="CAPILLARY">Capillary sequencing</option>
182 </param> 178 </param>
183 <param name="instrument_model" type="select" label="Instrument model"> 179 <param name="instrument_model" type="select" label="Instrument model">
184 <options from_data_table="instrument_model"> 180 <options from_data_table="instrument_model">
185 <column name="value" index="0"/> 181 <column name="value" index="0"/>
186 </options> 182 </options>
187 </param> 183 </param>
188 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 184 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
189 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> 185 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
190 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 186 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="File(s) associated with this run"/>
191 </repeat> 187 </repeat>
192 </repeat> 188 </repeat>
193 </repeat> 189 </repeat>
194 </repeat> 190 </repeat>
195 </xml> 191 </xml>
196 <xml name="nonviral_samples"> 192 <xml name="nonviral_samples">
197 <repeat name="rep_study" title="Study" min="1"> 193 <repeat name="rep_study" title="Study" min="1">
198 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> 194 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
199 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> 195 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
200 <param name="study_type" type="select" label="Please select the type of study"> 196 <param name="study_type" type="select" label="Please select the type of study">
201 <options from_data_table="study_type"> 197 <options from_data_table="study_type">
202 <column name="value" index="0"/> 198 <column name="value" index="0"/>
203 </options> 199 </options>
204 </param> 200 </param>
205 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> 201 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
206 <repeat name="rep_sample" title="Samples associated with this study" min="1" > 202 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
207 <param name="sample_title" type="text" label="Sample title"/> 203 <param name="sample_title" type="text" label="Sample title"/>
208 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> 204 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
209 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/> 205 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
210 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" /> 206 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
211 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > 207 <param name="collection_date" type="text" label="Collection date" optional="True" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
212 <param name="experiment_title" type="text" label="Specify an experiment title" /> 208 <option value="not collected">not collected</option>
213 <param name="experiment_design" type="text" label="Describe the experiment design" /> 209 <option value="restricted access">restricted access</option>
214 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library"> 210 <option value="not provided">not provided</option>
215 <options from_data_table="library_strategy"> 211 <validator type="regex" message="Data format is not valid">(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not collected$)|(^not provided$)|(^restricted access$)</validator>
216 <column name="value" index="0"/> 212 </param>
217 </options> 213 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
218 </param> 214 <options from_data_table="geographic_location_1">
219 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced"> 215 <column name="value" index="0"/>
220 <options from_data_table="library_source"> 216 </options>
221 <column name="value" index="0"/> 217 </param>
222 </options> 218 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
223 </param> 219 <param name="experiment_title" type="text" label="Specify an experiment title" />
224 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced"> 220 <param name="experiment_design" type="text" label="Describe the experiment design" />
225 <options from_data_table="library_selection"> 221 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
226 <column name="value" index="0"/> 222 <options from_data_table="library_strategy">
227 </options> 223 <column name="value" index="0"/>
228 </param> 224 </options>
229 <param name="library_layout" type="select" label="Library layout"> 225 </param>
230 <options from_data_table="library_layout"> 226 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
231 <column name="value" index="0"/> 227 <options from_data_table="library_source">
232 </options> 228 <column name="value" index="0"/>
233 </param> 229 </options>
234 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> 230 </param>
235 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> 231 <param name="library_selection" type="select" label="Library selection" help="The library selection specifies whether any method was used to select for or against, enrich, or screen the material being sequenced">
236 <param name="platform" type="select" label="Select the sequencing platform used"> 232 <options from_data_table="library_selection">
237 <option value="LS454">LS454</option> 233 <column name="value" index="0"/>
238 <option value="ILLUMINA" selected="True">Illumina</option> 234 </options>
239 <option value="HELICOS">Helicos</option> 235 </param>
240 <option value="ABI_SOLID">ABI Solid</option> 236 <param name="library_layout" type="select" label="Library layout">
241 <option value="COMPLETE_GENOMICS">Complete Genomics</option> 237 <options from_data_table="library_layout">
242 <option value="BGISEQ">BGI Seq</option> 238 <column name="value" index="0"/>
243 <option value="OXFORD_NANOPORE">Oxford Nanopore</option> 239 </options>
244 <option value="PACBIO_SMRT">PacBio</option> 240 </param>
245 <option value="ION_TORRENT">Ion Torrent</option> 241 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
246 <option value="CAPILLARY">Capillary sequencing</option> 242 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
247 </param> 243 <param name="platform" type="select" label="Select the sequencing platform used">
248 <param name="instrument_model" type="select" label="Instrument model"> 244 <options from_data_table="platform">
249 <options from_data_table="instrument_model"> 245 <column name="value" index="0"/>
250 <column name="value" index="0"/> 246 </options>
251 </options> 247 </param>
252 </param> 248 <param name="instrument_model" type="select" label="Instrument model">
253 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 249 <options from_data_table="instrument_model">
254 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/> 250 <column name="value" index="0"/>
255 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 251 </options>
252 </param>
253 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
254 <param name="run_base_name" type="text" optional="False" value="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
255 <param name="upload_files" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="File(s) associated with this run"/>
256 </repeat>
256 </repeat> 257 </repeat>
257 </repeat> 258 </repeat>
258 </repeat> 259 </repeat>
259 </repeat>
260 </xml> 260 </xml>
261 </macros> 261 </macros>