Mercurial > repos > iuc > ena_upload

annotate samples_macros.xml @ 12:29648e5e83a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 305061c25b6fcf54d960f17c2cad15c30fb2e26a-dirty
author iuc
date Wed, 27 Mar 2024 11:54:25 +0000
parents f803a68fc9e5
children ea5e944f447d
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1 <macros>
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2 <xml name="checklist_input_macro">
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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">
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4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option>
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5 <option value="ERC000012">GSC MIxS air (ERC000012)</option>
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6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option>
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7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option>
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8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option>
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9 <option value="ERC000016">GSC MIxS human oral (ERC000016)</option>
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10 <option value="ERC000017">GSC MIxS human skin (ERC000017)</option>
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11 <option value="ERC000018">GSC MIxS human vaginal (ERC000018)</option>
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12 <option value="ERC000019">GSC MIxS microbial mat biolfilm (ERC000019)</option>
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13 <option value="ERC000020">GSC MIxS plant associated (ERC000020)</option>
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14 <option value="ERC000021">GSC MIxS sediment (ERC000021)</option>
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15 <option value="ERC000022">GSC MIxS soil (ERC000022)</option>
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16 <option value="ERC000023">GSC MIxS wastewater sludge (ERC000023)</option>
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17 <option value="ERC000024">GSC MIxS water (ERC000024)</option>
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18 <option value="ERC000025">GSC MIxS miscellaneous natural or artificial environment (ERC000025)</option>
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19 <option value="ERC000027">ENA Micro B3 (ERC000027)</option>
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20 <option value="ERC000028">ENA prokaryotic pathogen minimal sample checklist (ERC000028)</option>
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21 <option value="ERC000029">ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1 (ERC000029)</option>
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22 <option value="ERC000030">ENA Tara Oceans (ERC000030)</option>
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23 <option value="ERC000031">GSC MIxS built environment (ERC000031)</option>
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24 <option value="ERC000032">ENA Influenza virus reporting standard checklist (ERC000032)</option>
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25 <option value="ERC000033">ENA virus pathogen reporting standard checklist (ERC000033)</option>
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26 <option value="ERC000034">ENA mutagenesis by carcinogen treatment checklist (ERC000034)</option>
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27 <option value="ERC000035">ENA Crop Plant sample enhanced annotation checklist (ERC000035)</option>
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28 <option value="ERC000036">ENA sewage checklist (ERC000036)</option>
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29 <option value="ERC000037">ENA Plant Sample Checklist (ERC000037)</option>
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30 <option value="ERC000038">ENA Shellfish Checklist (ERC000038)</option>
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31 <option value="ERC000039">ENA parasite sample checklist (ERC000039)</option>
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32 <option value="ERC000040">ENA UniEuk_EukBank Checklist (ERC000040)</option>
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33 <option value="ERC000041">ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist (ERC000041)</option>
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34 <option value="ERC000043">ENA Marine Microalgae Checklist (ERC000043)</option>
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35 <option value="ERC000044">COMPARE-ECDC-EFSA pilot human-associated reporting standard (ERC000044)</option>
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36 <option value="ERC000045">COMPARE-ECDC-EFSA pilot food-associated reporting standard (ERC000045)</option>
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37 <option value="ERC000047">GSC MIMAGS (ERC000047)</option>
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38 <option value="ERC000048">GSC MISAGS (ERC000048)</option>
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39 <option value="ERC000049">GSC MIUVIGS (ERC000049)</option>
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40 <option value="ERC000050">ENA binned metagenome (ERC000050)</option>
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41 <option value="ERC000051">PDX Checklist (ERC000051)</option>
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42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option>
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43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option>
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44 </param>
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45 </xml>
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46 <xml name="test_submit_section">
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47 <section name="test_submit_parameters" expanded="True" title="Submissions options">
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48 <param name="center" type="text" optional="False" label="Affiliation center"/>
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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/." />
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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."/>
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51 </section>
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52 </xml>
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53 <xml name="run_inputs_macro">
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54 <conditional name="run_input_format_conditional">
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55 <param name="run_input_format" type="select" label="Select input data">
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56 <option value="multiple_selection_list" selected="True">Dataset or dataset collection</option>
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57 <option value="paired_list" selected="False">Paired dataset collection</option>
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58 </param>
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59 <when value="multiple_selection_list">
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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?"/>
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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"/>
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62 </when>
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63 <when value="paired_list">
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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" />
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65 </when>
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66 </conditional>
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67 </xml>
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68 <xml name="table_inputs_macro">
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69 <conditional name="input_format_conditional">
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70 <param name="input_format" type="select" label="Select the metadata input method">
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71 <option value="excel_tables" selected="True">Excel file</option>
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72 <option value="user_generated_tables" selected="False">Tabular files (studies - samples - experiments - runs)</option>
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73 <option value="isa_json" selected="False">ISA json file</option>
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74 <option value="build_tables" selected="False">Interactively (only recommended for small studies)</option>
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75 </param>
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76 <when value="excel_tables">
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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)" />-->
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78 <expand macro="checklist_input_macro"/>
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79 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (.xlsx) file based on template" />
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80 <expand macro="run_inputs_macro" />
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81 </when>
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82 <when value="user_generated_tables">
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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)" />-->
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84 <expand macro="checklist_input_macro"/>
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85 <expand macro="run_inputs_macro" />
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86 <param name="studies_users_table" type="data" format="tabular" multiple="False" label="Studies table" help="Studies metadata file"/>
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87 <param name="samples_users_table" type="data" format="tabular" multiple="False" label="Samples table" help="Samples metadata file"/>
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88 <param name="experiments_users_table" type="data" format="tabular" multiple="False" label="Experiments table" help="Experiments metadata file"/>
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89 <param name="runs_users_table" type="data" format="tabular" multiple="False" label="Runs table" help="Runs metadata file"/>
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90 </when>
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91 <when value="build_tables">
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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?"/>
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93 <conditional name="conditional_viral_metadata">
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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.">
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95 <option value="True" selected="True">Viral</option>
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96 <option value="False" selected="False">Non viral</option>
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97 </param>
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98 <when value="True">
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99 <expand macro="viral_samples" />
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100 </when>
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101 <when value="False">
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102 <expand macro="nonviral_samples" />
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103 </when>
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104 </conditional>
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105 </when>
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106 <when value="isa_json">
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107 <param name="isa_json_file" type="data" format="json" label="Select ISA json file" />
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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)" />
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109 <expand macro="run_inputs_macro" />
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110 </when>
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111 </conditional>
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112
0
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113 </xml>
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114 <xml name="viral_samples">
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115 <repeat name="rep_study" title="Study" min="1">
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116 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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117 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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118 <param name="study_type" type="select" label="Please select the type of study">
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119 <options from_data_table="study_type">
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120 <column name="value" index="0"/>
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121 </options>
0
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122 </param>
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123 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
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124 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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125 <param name="sample_title" type="text" label="Sample title"/>
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126 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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127 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
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128 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
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129 <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">
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130 <option value="not collected">not collected</option>
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131 <option value="restricted access">restricted access</option>
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132 <option value="not provided">not provided</option>
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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>
0
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134 </param>
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135 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
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136 <options from_data_table="geographic_location_1">
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137 <column name="value" index="0"/>
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138 </options>
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139 </param>
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140 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/>
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141 <param name="host_subject_id" type="text" label="Host subject id"/>
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142 <param name="host_health_state" type="select" label="Host health state">
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143 <options from_data_table="host_health_state_1">
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144 <column name="value" index="0"/>
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145 </options>
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146 </param>
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147 <param name="host_sex" type="select" label="Host sex">
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148 <options from_data_table="host_sex_1">
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149 <column name="value" index="0"/>
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150 </options>
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151 </param>
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152 <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/>
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153 <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/>
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154 <param name="collecting_institution" type="text" label="Collecting institution"/>
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155 <param name="isolate" type="text" label="Isolate"/>
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156 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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157 <param name="experiment_title" type="text" label="Specify an experiment title" />
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158 <param name="experiment_design" type="text" label="Describe the experiment design" />
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159 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
0
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160 <options from_data_table="library_strategy">
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161 <column name="value" index="0"/>
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162 </options>
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163 </param>
10
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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">
0
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165 <options from_data_table="library_source">
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166 <column name="value" index="0"/>
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167 </options>
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168 </param>
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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">
0
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170 <options from_data_table="library_selection">
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171 <column name="value" index="0"/>
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172 </options>
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173 </param>
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174 <param name="library_layout" type="select" label="Library layout">
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175 <options from_data_table="library_layout">
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176 <column name="value" index="0"/>
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177 </options>
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178 </param>
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179 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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180 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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181 <param name="platform" type="select" label="Select the sequencing platform used">
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182 <options from_data_table="platform">
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183 <column name="value" index="0"/>
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184 </options>
0
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185 </param>
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186 <param name="instrument_model" type="select" label="Instrument model">
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187 <options from_data_table="instrument_model">
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188 <column name="value" index="0"/>
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189 </options>
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190 </param>
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191 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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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"/>
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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"/>
0
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194 </repeat>
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195 </repeat>
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196 </repeat>
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197 </repeat>
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198 </xml>
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199 <xml name="nonviral_samples">
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200 <repeat name="rep_study" title="Study" min="1">
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201 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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202 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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203 <param name="study_type" type="select" label="Please select the type of study">
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204 <options from_data_table="study_type">
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205 <column name="value" index="0"/>
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206 </options>
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207 </param>
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208 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
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209 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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210 <param name="sample_title" type="text" label="Sample title"/>
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211 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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212 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
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213 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" />
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214 <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">
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215 <option value="not collected">not collected</option>
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216 <option value="restricted access">restricted access</option>
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217 <option value="not provided">not provided</option>
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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>
0
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219 </param>
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220 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
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221 <options from_data_table="geographic_location_1">
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222 <column name="value" index="0"/>
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223 </options>
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224 </param>
10
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225 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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226 <param name="experiment_title" type="text" label="Specify an experiment title" />
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227 <param name="experiment_design" type="text" label="Describe the experiment design" />
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228 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
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229 <options from_data_table="library_strategy">
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230 <column name="value" index="0"/>
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231 </options>
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232 </param>
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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">
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234 <options from_data_table="library_source">
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235 <column name="value" index="0"/>
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236 </options>
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237 </param>
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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">
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239 <options from_data_table="library_selection">
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240 <column name="value" index="0"/>
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241 </options>
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242 </param>
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243 <param name="library_layout" type="select" label="Library layout">
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244 <options from_data_table="library_layout">
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245 <column name="value" index="0"/>
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246 </options>
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247 </param>
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248 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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249 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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250 <param name="platform" type="select" label="Select the sequencing platform used">
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251 <options from_data_table="platform">
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252 <column name="value" index="0"/>
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253 </options>
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254 </param>
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255 <param name="instrument_model" type="select" label="Instrument model">
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256 <options from_data_table="instrument_model">
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257 <column name="value" index="0"/>
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258 </options>
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259 </param>
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260 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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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"/>
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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"/>
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263 </repeat>
0
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264 </repeat>
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265 </repeat>
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266 </repeat>
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267 </xml>
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268 </macros>
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269