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comparison samples_macros.xml @ 10:e7995727674f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
author iuc
date Mon, 27 Jan 2025 18:12:01 +0000
parents ae2d35b56645
children
comparison
equal deleted inserted replaced
9:69fc9c4a68b7 10:e7995727674f
1 <macros> 1 <macros>
2 <xml name="checklist_input_macro"> 2 <xml name="checklist_input_macro">
3 <param type="select" name="checklist_id" label="Select the metadata checklist" help="You can find metadata templates for each checklist at: https://github.com/ELIXIR-Belgium/ENA-metadata-templates"> 3 <param type="select" name="checklist_id" label="Select the ENA sample checklist" help="You can find metadata templates for each checklist at: https://github.com/ELIXIR-Belgium/ENA-metadata-templates">
4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option> 4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option>
5 <option value="ERC000012">GSC MIxS air (ERC000012)</option> 5 <option value="ERC000012">GSC MIxS air (ERC000012)</option>
6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option> 6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option>
7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option> 7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option>
8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option> 8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option>
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="Submissions 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="center" type="text" optional="False" label="Affiliation center"/>
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="submit_dev" type="boolean" truevalue="True" falsevalue="False" label="Submit to ENA test server" help="Uploads to the test server of ENA will not be made public and will be removed automatically in 24 hours. Performing a preliminary test upload is advised to check for errors with metadata structure. You can find these uploads at https://wwwdev.ebi.ac.uk/ena/." />
50 <param name="dry_run" type="boolean" truevalue="True" falsevalue="False" label="Create test outputs without submitting (meta)data to ENA" help="If yes is selected then NO submission will be performed."/>
50 </section> 51 </section>
51 </xml> 52 </xml>
52 <xml name="run_inputs_macro"> 53 <xml name="run_inputs_macro">
53 <conditional name="run_input_format_conditional"> 54 <conditional name="run_input_format_conditional">
54 <param name="run_input_format" type="select" label="Select runs input format"> 55 <param name="run_input_format" type="select" label="Select input data">
55 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> 56 <option value="multiple_selection_list" selected="True">Dataset or dataset collection</option>
56 <option value="paired_list" selected="False">Input from a paired collection</option> 57 <option value="paired_list" selected="False">Paired dataset collection</option>
57 </param> 58 </param>
58 <when value="multiple_selection_list"> 59 <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?"/> 60 <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"/> 61 <param name="data" type="data" format="fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fastq.gz,fastq.bz2" multiple="True" label="Select dataset or dataset collection" help="Names should match the compressed run's files names defined in the metadata"/>
61 </when> 62 </when>
62 <when value="paired_list"> 63 <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" /> 64 <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 sequencing data files" help="Names should match the compressed run's files names defined in the metadata" />
64 </when> 65 </when>
65 </conditional> 66 </conditional>
66 </xml> 67 </xml>
67 <xml name="table_inputs_macro"> 68 <xml name="table_inputs_macro">
68 <conditional name="input_format_conditional"> 69 <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?"> 70 <param name="input_format" type="select" label="Select the metadata input method">
70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option> 71 <option value="excel_tables" selected="True">Excel file</option>
71 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> 72 <option value="user_generated_tables" selected="False">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 <option value="isa_json" selected="False">ISA json file</option>
74 <option value="build_tables" selected="False">Interactively (only recommended for small studies)</option>
73 </param> 75 </param>
74 <when value="excel_tables"> 76 <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)" />--> 77 <!--<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"/> 78 <expand macro="checklist_input_macro"/>
77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" /> 79 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (.xlsx) file based on template" />
78 <expand macro="run_inputs_macro" /> 80 <expand macro="run_inputs_macro" />
79 </when> 81 </when>
80 <when value="user_generated_tables"> 82 <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)" />--> 83 <!--<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"/> 84 <expand macro="checklist_input_macro"/>
83 <expand macro="run_inputs_macro" /> 85 <expand macro="run_inputs_macro" />
84 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> 86 <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"/> 87 <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"/> 88 <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"/> 89 <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/>
88 </when> 90 </when>
89 <when value="build_tables"> 91 <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?"/> 92 <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"> 93 <conditional name="conditional_viral_metadata">
92 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" /> 94 <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"> 95 <option value="True" selected="True">Viral</option>
96 <option value="False" selected="False">Non viral</option>
97 </param>
98 <when value="True">
94 <expand macro="viral_samples" /> 99 <expand macro="viral_samples" />
95 </when> 100 </when>
96 <when value="false"> 101 <when value="False">
97 <expand macro="nonviral_samples" /> 102 <expand macro="nonviral_samples" />
98 </when> 103 </when>
99 </conditional> 104 </conditional>
100 </when> 105 </when>
106 <when value="isa_json">
107 <param name="isa_json_file" type="data" format="json" label="Select ISA json file" />
108 <param name="isa_assay_stream" type="text" optional="False" help="List the assay_stream values from the comment field in the assays list of the ISA-json you want to submit." label="Specify the ISA json assay stream(s)" />
109 <expand macro="run_inputs_macro" />
110 </when>
101 </conditional> 111 </conditional>
102 <param name="center" type="text" optional="False" label="Affiliation center"/> 112
103 </xml> 113 </xml>
104 <xml name="viral_samples"> 114 <xml name="viral_samples">
105 <repeat name="rep_study" title="Study" min="1"> 115 <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"/> 116 <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"/> 117 <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"> 118 <param name="study_type" type="select" label="Please select the type of study">
109 <options from_data_table="study_type"> 119 <options from_data_table="study_type">
110 <column name="value" index="0"/> 120 <column name="value" index="0"/>
111 </options> 121 </options>
112 </param> 122 </param>
113 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> 123 <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" > 124 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
115 <param name="sample_title" type="text" label="Sample title"/> 125 <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"/> 126 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
117 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/> 127 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
118 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" /> 128 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
119 <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"> 129 <param name="collection_date" type="text" label="Collection date" optional="False" help="options are: YYYY, YYYY-MM, YYYY-MM-DD, not collected, restricted access or not provided">
120 <option value="not collected">not collected</option> 130 <option value="not collected">not collected</option>
121 <option value="restricted access">restricted access</option> 131 <option value="restricted access">restricted access</option>
122 <option value="not provided">not provided</option> 132 <option value="not provided">not provided</option>
123 <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> 133 <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>
124 </param> 134 </param>
125 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained"> 135 <param name="geo_location_country" type="select" optional="False" label="Select the country where the sample was obtained">
126 <options from_data_table="geographic_location_1"> 136 <options from_data_table="geographic_location_1">
127 <column name="value" index="0"/> 137 <column name="value" index="0"/>
128 </options> 138 </options>
129 </param> 139 </param>
130 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/> 140 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/>
144 <param name="collecting_institution" type="text" label="Collecting institution"/> 154 <param name="collecting_institution" type="text" label="Collecting institution"/>
145 <param name="isolate" type="text" label="Isolate"/> 155 <param name="isolate" type="text" label="Isolate"/>
146 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > 156 <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" /> 157 <param name="experiment_title" type="text" label="Specify an experiment title" />
148 <param name="experiment_design" type="text" label="Describe the experiment design" /> 158 <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"> 159 <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"> 160 <options from_data_table="library_strategy">
151 <column name="value" index="0"/> 161 <column name="value" index="0"/>
152 </options> 162 </options>
153 </param> 163 </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"> 164 <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"> 165 <options from_data_table="library_source">
156 <column name="value" index="0"/> 166 <column name="value" index="0"/>
157 </options> 167 </options>
158 </param> 168 </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"> 169 <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"> 170 <options from_data_table="library_selection">
161 <column name="value" index="0"/> 171 <column name="value" index="0"/>
162 </options> 172 </options>
163 </param> 173 </param>
164 <param name="library_layout" type="select" label="Library layout"> 174 <param name="library_layout" type="select" label="Library layout">
167 </options> 177 </options>
168 </param> 178 </param>
169 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> 179 <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"/> 180 <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"> 181 <param name="platform" type="select" label="Select the sequencing platform used">
172 <option value="LS454">LS454</option> 182 <options from_data_table="platform">
173 <option value="ILLUMINA">Illumina</option> 183 <column name="value" index="0"/>
174 <option value="HELICOS">Helicos</option> 184 </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> 185 </param>
183 <param name="instrument_model" type="select" label="Instrument model"> 186 <param name="instrument_model" type="select" label="Instrument model">
184 <options from_data_table="instrument_model"> 187 <options from_data_table="instrument_model">
185 <column name="value" index="0"/> 188 <column name="value" index="0"/>
186 </options> 189 </options>
187 </param> 190 </param>
188 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 191 <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"/> 192 <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"/> 193 <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> 194 </repeat>
192 </repeat> 195 </repeat>
193 </repeat> 196 </repeat>
194 </repeat> 197 </repeat>
195 </xml> 198 </xml>
196 <xml name="nonviral_samples"> 199 <xml name="nonviral_samples">
197 <repeat name="rep_study" title="Study" min="1"> 200 <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"/> 201 <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"/> 202 <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"> 203 <param name="study_type" type="select" label="Please select the type of study">
201 <options from_data_table="study_type"> 204 <options from_data_table="study_type">
202 <column name="value" index="0"/> 205 <column name="value" index="0"/>
203 </options> 206 </options>
204 </param> 207 </param>
205 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> 208 <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" > 209 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
207 <param name="sample_title" type="text" label="Sample title"/> 210 <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"/> 211 <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"/> 212 <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" /> 213 <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" > 214 <param name="collection_date" type="text" label="Collection date" optional="False" 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" /> 215 <option value="not collected">not collected</option>
213 <param name="experiment_design" type="text" label="Describe the experiment design" /> 216 <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"> 217 <option value="not provided">not provided</option>
215 <options from_data_table="library_strategy"> 218 <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"/> 219 </param>
217 </options> 220 <param name="geo_location_country" type="select" optional="False" label="Select the country where the sample was obtained">
218 </param> 221 <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"> 222 <column name="value" index="0"/>
220 <options from_data_table="library_source"> 223 </options>
221 <column name="value" index="0"/> 224 </param>
222 </options> 225 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
223 </param> 226 <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"> 227 <param name="experiment_design" type="text" label="Describe the experiment design" />
225 <options from_data_table="library_selection"> 228 <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"/> 229 <options from_data_table="library_strategy">
227 </options> 230 <column name="value" index="0"/>
228 </param> 231 </options>
229 <param name="library_layout" type="select" label="Library layout"> 232 </param>
230 <options from_data_table="library_layout"> 233 <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"/> 234 <options from_data_table="library_source">
232 </options> 235 <column name="value" index="0"/>
233 </param> 236 </options>
234 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> 237 </param>
235 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> 238 <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"> 239 <options from_data_table="library_selection">
237 <option value="LS454">LS454</option> 240 <column name="value" index="0"/>
238 <option value="ILLUMINA" selected="True">Illumina</option> 241 </options>
239 <option value="HELICOS">Helicos</option> 242 </param>
240 <option value="ABI_SOLID">ABI Solid</option> 243 <param name="library_layout" type="select" label="Library layout">
241 <option value="COMPLETE_GENOMICS">Complete Genomics</option> 244 <options from_data_table="library_layout">
242 <option value="BGISEQ">BGI Seq</option> 245 <column name="value" index="0"/>
243 <option value="OXFORD_NANOPORE">Oxford Nanopore</option> 246 </options>
244 <option value="PACBIO_SMRT">PacBio</option> 247 </param>
245 <option value="ION_TORRENT">Ion Torrent</option> 248 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
246 <option value="CAPILLARY">Capillary sequencing</option> 249 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
247 </param> 250 <param name="platform" type="select" label="Select the sequencing platform used">
248 <param name="instrument_model" type="select" label="Instrument model"> 251 <options from_data_table="platform">
249 <options from_data_table="instrument_model"> 252 <column name="value" index="0"/>
250 <column name="value" index="0"/> 253 </options>
251 </options> 254 </param>
252 </param> 255 <param name="instrument_model" type="select" label="Instrument model">
253 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > 256 <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"/> 257 <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"/> 258 </options>
259 </param>
260 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
261 <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"/>
262 <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"/>
263 </repeat>
256 </repeat> 264 </repeat>
257 </repeat> 265 </repeat>
258 </repeat> 266 </repeat>
259 </repeat>
260 </xml> 267 </xml>
261 </macros> 268 </macros>