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comparison samples_macros.xml @ 1:bd624f0547fc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
author iuc
date Fri, 30 Apr 2021 12:08:48 +0000
parents b7356ece7ceb
children 982757f4aa8c
comparison
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0:b7356ece7ceb 1:bd624f0547fc
1 <macros> 1 <macros>
2 2 <xml name="test_submit_section">
3 <section name="test_submit_parameters" expanded="true" title="Testing options">
4 <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/" />
5 <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."/>
6 </section>
7 </xml>
8 <xml name="run_inputs_macro">
9 <conditional name="run_input_format_conditional">
10 <param name="run_input_format" type="select" label="Select runs input format">
11 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
12 <option value="paired_list" selected="False">Input from a paired collection</option>
13 </param>
14 <when value="multiple_selection_list">
15 <param name="data" type="data" format="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"/>
16 </when>
17 <when value="paired_list">
18 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="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" />
19 </when>
20 </conditional>
21 </xml>
3 <xml name="table_inputs_macro"> 22 <xml name="table_inputs_macro">
4 <conditional name="input_format_conditional"> 23 <conditional name="input_format_conditional">
5 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?"> 24 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
6 <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option> 25 <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option>
7 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> 26 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
8 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> 27 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
9 </param> 28 </param>
10 <when value="excel_tables"> 29 <when value="excel_tables">
11 <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)" /> 30 <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)" />
12 <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/> 31 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" />
13 <param name="xlsx_file" type="data" format="xlsx" /> 32 <expand macro="run_inputs_macro" />
14 <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/>
15 </when> 33 </when>
16 <when value="user_generated_tables"> 34 <when value="user_generated_tables">
17 <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)" /> 35 <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)" />
18 <param name="data" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="Select all datasets to upload" help="Compressed reads files listed in the runs table"/> 36 <expand macro="run_inputs_macro" />
19 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> 37 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/>
20 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> 38 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
21 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> 39 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
22 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> 40 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
23 </when> 41 </when>
24 <when value="build_tables"> 42 <when value="build_tables">
25 <param name="dry_run" type="boolean" label="Print the tables but do not submit the datasets" help="If yes is selected then NO submission will be performed."/>
26 <conditional name="conditional_viral_metadata"> 43 <conditional name="conditional_viral_metadata">
27 <param name="viral_sample" type="boolean" label="Does your submission contains viral samples?" /> 44 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
28 <when value="true"> 45 <when value="true">
29 <expand macro="viral_samples" /> 46 <expand macro="viral_samples" />
30 </when> 47 </when>
31 <when value="false"> 48 <when value="false">
32 <expand macro="nonviral_samples" /> 49 <expand macro="nonviral_samples" />
49 <repeat name="rep_sample" title="Samples associated with this study" min="1" > 66 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
50 <param name="sample_title" type="text" label="Sample title"/> 67 <param name="sample_title" type="text" label="Sample title"/>
51 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> 68 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
52 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/> 69 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
53 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" /> 70 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
54 <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 leave blank"> 71 <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">
55 <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})?)?)?)?)?$)|(^not colected$)|(^not provided$)|(^restricted access$)</validator> 72 <option value="not collected">not collected</option>
73 <option value="restricted access">restricted access</option>
74 <option value="not provided">not provided</option>
75 <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>
56 </param> 76 </param>
57 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained"> 77 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
58 <options from_data_table="geographic_location_1"> 78 <options from_data_table="geographic_location_1">
59 <column name="value" index="0"/> 79 <column name="value" index="0"/>
60 </options> 80 </options>
116 <options from_data_table="instrument_model"> 136 <options from_data_table="instrument_model">
117 <column name="value" index="0"/> 137 <column name="value" index="0"/>
118 </options> 138 </options>
119 </param> 139 </param>
120 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 140 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
141 <param name="run_base_name" type="text" optional="False" default="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
121 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 142 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
122 </repeat> 143 </repeat>
123 </repeat> 144 </repeat>
124 </repeat> 145 </repeat>
125 </repeat> 146 </repeat>
164 </param> 185 </param>
165 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> 186 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
166 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> 187 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
167 <param name="platform" type="select" label="Select the sequencing platform used"> 188 <param name="platform" type="select" label="Select the sequencing platform used">
168 <option value="LS454">LS454</option> 189 <option value="LS454">LS454</option>
169 <option value="ILLUMINA">Illumina</option> 190 <option value="ILLUMINA" selected="True">Illumina</option>
170 <option value="HELICOS">Helicos</option> 191 <option value="HELICOS">Helicos</option>
171 <option value="ABI_SOLID">ABI Solid</option> 192 <option value="ABI_SOLID">ABI Solid</option>
172 <option value="COMPLETE_GENOMICS">Complete Genomics</option> 193 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
173 <option value="BGISEQ">BGI Seq</option> 194 <option value="BGISEQ">BGI Seq</option>
174 <option value="OXFORD_NANOPORE">Oxford Nanopore</option> 195 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
180 <options from_data_table="instrument_model"> 201 <options from_data_table="instrument_model">
181 <column name="value" index="0"/> 202 <column name="value" index="0"/>
182 </options> 203 </options>
183 </param> 204 </param>
184 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 205 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
206 <param name="run_base_name" type="text" optional="False" default="" label="Run alias" help="If an alias is not provided it will be generated combining the sample and experiment indexes"/>
185 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/> 207 <param name="upload_files" type="data" format="fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="true" label="File(s) associated with this run"/>
186 </repeat> 208 </repeat>
187 </repeat> 209 </repeat>
188 </repeat> 210 </repeat>
189 </repeat> 211 </repeat>