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comparison samples_macros.xml @ 0:382518f24d6d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
author iuc
date Sat, 28 Nov 2020 09:45:44 +0000
parents
children 57251c760cab
comparison
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-1:000000000000 0:382518f24d6d
1 <macros>
2
3 <xml name="table_inputs_macro">
4 <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?">
6 <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>
8 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option>
9 </param>
10 <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)" />
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."/>
13 <param name="xlsx_file" type="data" format="xlsx" />
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>
16 <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)" />
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"/>
19 <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"/>
21 <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"/>
23 </when>
24 <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">
27 <param name="viral_sample" type="boolean" label="Does your submission contains viral samples?" />
28 <when value="true">
29 <expand macro="viral_samples" />
30 </when>
31 <when value="false">
32 <expand macro="nonviral_samples" />
33 </when>
34 </conditional>
35 </when>
36 </conditional>
37 <param name="center" type="text" optional="False" label="Affiliation center"/>
38 </xml>
39 <xml name="viral_samples">
40 <repeat name="rep_study" title="Study" min="1">
41 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
42 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
43 <param name="study_type" type="select" label="Please select the type of study">
44 <options from_data_table="study_type">
45 <column name="value" index="0"/>
46 </options>
47 </param>
48 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
49 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
50 <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"/>
52 <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" />
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">
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>
56 </param>
57 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained">
58 <options from_data_table="geographic_location_1">
59 <column name="value" index="0"/>
60 </options>
61 </param>
62 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/>
63 <param name="host_subject_id" type="text" label="Host subject id"/>
64 <param name="host_health_state" type="select" label="Host health state">
65 <options from_data_table="host_health_state_1">
66 <column name="value" index="0"/>
67 </options>
68 </param>
69 <param name="host_sex" type="select" label="Host sex">
70 <options from_data_table="host_sex_1">
71 <column name="value" index="0"/>
72 </options>
73 </param>
74 <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/>
75 <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/>
76 <param name="collecting_institution" type="text" label="Collecting institution"/>
77 <param name="isolate" type="text" label="Isolate"/>
78 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
79 <param name="experiment_title" type="text" label="Specify an experiment title" />
80 <param name="experiment_design" type="text" label="Describe the experiment design" />
81 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
82 <options from_data_table="library_strategy">
83 <column name="value" index="0"/>
84 </options>
85 </param>
86 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
87 <options from_data_table="library_source">
88 <column name="value" index="0"/>
89 </options>
90 </param>
91 <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">
92 <options from_data_table="library_selection">
93 <column name="value" index="0"/>
94 </options>
95 </param>
96 <param name="library_layout" type="select" label="Library layout">
97 <options from_data_table="library_layout">
98 <column name="value" index="0"/>
99 </options>
100 </param>
101 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/>
102 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/>
103 <param name="platform" type="select" label="Select the sequencing platform used">
104 <option value="LS454">LS454</option>
105 <option value="ILLUMINA">Illumina</option>
106 <option value="HELICOS">Helicos</option>
107 <option value="ABI_SOLID">ABI Solid</option>
108 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
109 <option value="BGISEQ">BGI Seq</option>
110 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
111 <option value="PACBIO_SMRT">PacBio</option>
112 <option value="ION_TORRENT">Ion Torrent</option>
113 <option value="CAPILLARY">Capillary sequencing</option>
114 </param>
115 <param name="instrument_model" type="select" label="Instrument model">
116 <options from_data_table="instrument_model">
117 <column name="value" index="0"/>
118 </options>
119 </param>
120 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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"/>
122 </repeat>
123 </repeat>
124 </repeat>
125 </repeat>
126 </xml>
127 <xml name="nonviral_samples">
128 <repeat name="rep_study" title="Study" min="1">
129 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/>
130 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/>
131 <param name="study_type" type="select" label="Please select the type of study">
132 <options from_data_table="study_type">
133 <column name="value" index="0"/>
134 </options>
135 </param>
136 <param name="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/>
137 <repeat name="rep_sample" title="Samples associated with this study" min="1" >
138 <param name="sample_title" type="text" label="Sample title"/>
139 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/>
140 <param name="scientific_name" type="text" label="Enter the species of the sample" help="e.g Severe acute respiratory syndrome coronavirus 2"/>
141 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" />
142 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" >
143 <param name="experiment_title" type="text" label="Specify an experiment title" />
144 <param name="experiment_design" type="text" label="Describe the experiment design" />
145 <param name="library_strategy" type="select" label="Library strategy" help="The library strategy specifies the sequencing technique intended for this library">
146 <options from_data_table="library_strategy">
147 <column name="value" index="0"/>
148 </options>
149 </param>
150 <param name="library_source" type="select" label="Select library source" help="The library source specifies the type of source material that is being sequenced">
151 <options from_data_table="library_source">
152 <column name="value" index="0"/>
153 </options>
154 </param>
155 <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">
156 <options from_data_table="library_selection">
157 <column name="value" index="0"/>
158 </options>
159 </param>
160 <param name="library_layout" type="select" label="Library layout">
161 <options from_data_table="library_layout">
162 <column name="value" index="0"/>
163 </options>
164 </param>
165 <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"/>
167 <param name="platform" type="select" label="Select the sequencing platform used">
168 <option value="LS454">LS454</option>
169 <option value="ILLUMINA">Illumina</option>
170 <option value="HELICOS">Helicos</option>
171 <option value="ABI_SOLID">ABI Solid</option>
172 <option value="COMPLETE_GENOMICS">Complete Genomics</option>
173 <option value="BGISEQ">BGI Seq</option>
174 <option value="OXFORD_NANOPORE">Oxford Nanopore</option>
175 <option value="PACBIO_SMRT">PacBio</option>
176 <option value="ION_TORRENT">Ion Torrent</option>
177 <option value="CAPILLARY">Capillary sequencing</option>
178 </param>
179 <param name="instrument_model" type="select" label="Instrument model">
180 <options from_data_table="instrument_model">
181 <column name="value" index="0"/>
182 </options>
183 </param>
184 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" >
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"/>
186 </repeat>
187 </repeat>
188 </repeat>
189 </repeat>
190 </xml>
191 </macros>