Mercurial > repos > iuc > ena_upload

annotate samples_macros.xml @ 5:e1b3b37aa69f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit da03a9fa221bac18771fb317255cca9d89620f4b"
author iuc
date Wed, 27 Oct 2021 16:38:10 +0000
parents 26ccb678abc8
children 6f6537780379
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1 <macros>
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2 <xml name="test_submit_section">
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3 <section name="test_submit_parameters" expanded="true" title="Testing options">
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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/" />
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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."/>
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6 </section>
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7 </xml>
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8 <xml name="run_inputs_macro">
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9 <conditional name="run_input_format_conditional">
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10 <param name="run_input_format" type="select" label="Select runs input format">
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11 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option>
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12 <option value="paired_list" selected="False">Input from a paired collection</option>
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13 </param>
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14 <when value="multiple_selection_list">
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15 <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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16 <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"/>
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17 </when>
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18 <when value="paired_list">
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19 <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" />
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20 </when>
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21 </conditional>
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22 </xml>
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23 <xml name="table_inputs_macro">
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24 <conditional name="input_format_conditional">
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25 <param name="input_format" type="select" label="Would you like to submit pregenerated table files or interactively define the input structures?">
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26 <option value="excel_tables" selected="True">User generated metadata tables based on Excel templates</option>
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27 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option>
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28 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
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29 </param>
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30 <when value="excel_tables">
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31 <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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32 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on templates" />
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33 <expand macro="run_inputs_macro" />
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34 </when>
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35 <when value="user_generated_tables">
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36 <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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37 <expand macro="run_inputs_macro" />
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38 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/>
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39 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/>
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40 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/>
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41 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/>
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42 </when>
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43 <when value="build_tables">
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44 <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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45 <conditional name="conditional_viral_metadata">
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46 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" />
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47 <when value="true">
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48 <expand macro="viral_samples" />
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49 </when>
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50 <when value="false">
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51 <expand macro="nonviral_samples" />
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52 </when>
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53 </conditional>
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54 </when>
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55 </conditional>
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56 <param name="center" type="text" optional="False" label="Affiliation center"/>
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57 </xml>
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58 <xml name="viral_samples">
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59 <repeat name="rep_study" title="Study" min="1">
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60 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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61 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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62 <param name="study_type" type="select" label="Please select the type of study">
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63 <options from_data_table="study_type">
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64 <column name="value" index="0"/>
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65 </options>
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66 </param>
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67 <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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68 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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69 <param name="sample_title" type="text" label="Sample title"/>
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70 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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71 <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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72 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
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73 <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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74 <option value="not collected">not collected</option>
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75 <option value="restricted access">restricted access</option>
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76 <option value="not provided">not provided</option>
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77 <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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78 </param>
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79 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
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80 <options from_data_table="geographic_location_1">
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81 <column name="value" index="0"/>
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82 </options>
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83 </param>
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84 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/>
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85 <param name="host_subject_id" type="text" label="Host subject id"/>
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86 <param name="host_health_state" type="select" label="Host health state">
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87 <options from_data_table="host_health_state_1">
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88 <column name="value" index="0"/>
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89 </options>
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90 </param>
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91 <param name="host_sex" type="select" label="Host sex">
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92 <options from_data_table="host_sex_1">
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93 <column name="value" index="0"/>
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94 </options>
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95 </param>
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96 <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/>
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97 <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/>
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98 <param name="collecting_institution" type="text" label="Collecting institution"/>
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99 <param name="isolate" type="text" label="Isolate"/>
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100 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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101 <param name="experiment_title" type="text" label="Specify an experiment title" />
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102 <param name="experiment_design" type="text" label="Describe the experiment design" />
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103 <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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104 <options from_data_table="library_strategy">
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105 <column name="value" index="0"/>
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106 </options>
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107 </param>
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108 <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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109 <options from_data_table="library_source">
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110 <column name="value" index="0"/>
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111 </options>
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112 </param>
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113 <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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114 <options from_data_table="library_selection">
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115 <column name="value" index="0"/>
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116 </options>
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117 </param>
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118 <param name="library_layout" type="select" label="Library layout">
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119 <options from_data_table="library_layout">
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120 <column name="value" index="0"/>
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121 </options>
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122 </param>
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123 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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124 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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125 <param name="platform" type="select" label="Select the sequencing platform used">
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126 <option value="LS454">LS454</option>
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127 <option value="ILLUMINA">Illumina</option>
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128 <option value="HELICOS">Helicos</option>
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129 <option value="ABI_SOLID">ABI Solid</option>
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130 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
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131 <option value="BGISEQ">BGI Seq</option>
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132 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
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133 <option value="PACBIO_SMRT">PacBio</option>
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134 <option value="ION_TORRENT">Ion Torrent</option>
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135 <option value="CAPILLARY">Capillary sequencing</option>
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136 </param>
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137 <param name="instrument_model" type="select" label="Instrument model">
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138 <options from_data_table="instrument_model">
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139 <column name="value" index="0"/>
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140 </options>
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141 </param>
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142 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
4
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143 <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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144 <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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145 </repeat>
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146 </repeat>
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147 </repeat>
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148 </repeat>
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149 </xml>
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150 <xml name="nonviral_samples">
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151 <repeat name="rep_study" title="Study" min="1">
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152 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
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153 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
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154 <param name="study_type" type="select" label="Please select the type of study">
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155 <options from_data_table="study_type">
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156 <column name="value" index="0"/>
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157 </options>
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158 </param>
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159 <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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160 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
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161 <param name="sample_title" type="text" label="Sample title"/>
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162 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
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163 <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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164 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
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165 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
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166 <param name="experiment_title" type="text" label="Specify an experiment title" />
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167 <param name="experiment_design" type="text" label="Describe the experiment design" />
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168 <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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169 <options from_data_table="library_strategy">
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170 <column name="value" index="0"/>
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171 </options>
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172 </param>
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173 <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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174 <options from_data_table="library_source">
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175 <column name="value" index="0"/>
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176 </options>
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177 </param>
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178 <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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179 <options from_data_table="library_selection">
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180 <column name="value" index="0"/>
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181 </options>
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182 </param>
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183 <param name="library_layout" type="select" label="Library layout">
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184 <options from_data_table="library_layout">
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185 <column name="value" index="0"/>
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186 </options>
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187 </param>
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188 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
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189 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
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190 <param name="platform" type="select" label="Select the sequencing platform used">
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191 <option value="LS454">LS454</option>
1
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192 <option value="ILLUMINA" selected="True">Illumina</option>
0
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193 <option value="HELICOS">Helicos</option>
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194 <option value="ABI_SOLID">ABI Solid</option>
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195 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
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196 <option value="BGISEQ">BGI Seq</option>
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197 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
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198 <option value="PACBIO_SMRT">PacBio</option>
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199 <option value="ION_TORRENT">Ion Torrent</option>
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200 <option value="CAPILLARY">Capillary sequencing</option>
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201 </param>
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202 <param name="instrument_model" type="select" label="Instrument model">
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203 <options from_data_table="instrument_model">
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204 <column name="value" index="0"/>
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205 </options>
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206 </param>
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207 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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208 <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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209 <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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210 </repeat>
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211 </repeat>
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212 </repeat>
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213 </repeat>
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214 </xml>
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215 </macros>