Mercurial > repos > iuc > ena_upload
annotate samples_macros.xml @ 7:6f6537780379 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
| author | iuc |
|---|---|
| date | Thu, 24 Feb 2022 18:20:40 +0000 |
| parents | 26ccb678abc8 |
| children | 480d9e9d156b |
| rev | line source |
|---|---|
|
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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1 <macros> |
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7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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2 <xml name="checklist_input_macro"> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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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"> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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4 <option value="ERC000011">ENA default sample checklist (ERC000011)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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5 <option value="ERC000012">GSC MIxS air (ERC000012)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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6 <option value="ERC000013">GSC MIxS host associated (ERC000013)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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7 <option value="ERC000014">GSC MIxS human associated (ERC000014)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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8 <option value="ERC000015">GSC MIxS human gut (ERC000015)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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9 <option value="ERC000016">GSC MIxS human oral (ERC000016)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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10 <option value="ERC000017">GSC MIxS human skin (ERC000017)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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11 <option value="ERC000018">GSC MIxS human vaginal (ERC000018)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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12 <option value="ERC000019">GSC MIxS microbial mat biolfilm (ERC000019)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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13 <option value="ERC000020">GSC MIxS plant associated (ERC000020)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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14 <option value="ERC000021">GSC MIxS sediment (ERC000021)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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15 <option value="ERC000022">GSC MIxS soil (ERC000022)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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16 <option value="ERC000023">GSC MIxS wastewater sludge (ERC000023)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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17 <option value="ERC000024">GSC MIxS water (ERC000024)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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18 <option value="ERC000025">GSC MIxS miscellaneous natural or artificial environment (ERC000025)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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19 <option value="ERC000027">ENA Micro B3 (ERC000027)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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20 <option value="ERC000028">ENA prokaryotic pathogen minimal sample checklist (ERC000028)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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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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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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22 <option value="ERC000030">ENA Tara Oceans (ERC000030)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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23 <option value="ERC000031">GSC MIxS built environment (ERC000031)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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24 <option value="ERC000032">ENA Influenza virus reporting standard checklist (ERC000032)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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diff
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25 <option value="ERC000033">ENA virus pathogen reporting standard checklist (ERC000033)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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26 <option value="ERC000034">ENA mutagenesis by carcinogen treatment checklist (ERC000034)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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27 <option value="ERC000035">ENA Crop Plant sample enhanced annotation checklist (ERC000035)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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28 <option value="ERC000036">ENA sewage checklist (ERC000036)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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29 <option value="ERC000037">ENA Plant Sample Checklist (ERC000037)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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30 <option value="ERC000038">ENA Shellfish Checklist (ERC000038)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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31 <option value="ERC000039">ENA parasite sample checklist (ERC000039)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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32 <option value="ERC000040">ENA UniEuk_EukBank Checklist (ERC000040)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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33 <option value="ERC000041">ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist (ERC000041)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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34 <option value="ERC000043">ENA Marine Microalgae Checklist (ERC000043)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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35 <option value="ERC000044">COMPARE-ECDC-EFSA pilot human-associated reporting standard (ERC000044)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
4
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36 <option value="ERC000045">COMPARE-ECDC-EFSA pilot food-associated reporting standard (ERC000045)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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37 <option value="ERC000047">GSC MIMAGS (ERC000047)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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38 <option value="ERC000048">GSC MISAGS (ERC000048)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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39 <option value="ERC000049">GSC MIUVIGS (ERC000049)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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40 <option value="ERC000050">ENA binned metagenome (ERC000050)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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41 <option value="ERC000051">PDX Checklist (ERC000051)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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42 <option value="ERC000052">HoloFood Checklist (ERC000052)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
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43 <option value="ERC000053">Tree of Life Checklist (ERC000053)</option> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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44 </param> |
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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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45 </xml> |
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1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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46 <xml name="test_submit_section"> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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47 <section name="test_submit_parameters" expanded="true" title="Testing options"> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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/" /> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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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."/> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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50 </section> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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51 </xml> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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52 <xml name="run_inputs_macro"> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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53 <conditional name="run_input_format_conditional"> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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54 <param name="run_input_format" type="select" label="Select runs input format"> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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55 <option value="multiple_selection_list" selected="True">Select individual datasets or datasets collection</option> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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56 <option value="paired_list" selected="False">Input from a paired collection</option> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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57 </param> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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58 <when value="multiple_selection_list"> |
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26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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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?"/> |
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26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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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"/> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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61 </when> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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62 <when value="paired_list"> |
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26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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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" /> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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64 </when> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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65 </conditional> |
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57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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66 </xml> |
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382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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67 <xml name="table_inputs_macro"> |
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382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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68 <conditional name="input_format_conditional"> |
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382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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69 <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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6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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70 <option value="excel_tables" selected="True">User generated metadata tables based on Excel template</option> |
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71 <option value="build_tables" selected="False">Interactive generation of the study structure (recommended for small studies)</option> |
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72 <option value="user_generated_tables" selected="False">User generated tabular files (studies - samples - experiments - runs) </option> |
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73 </param> |
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74 <when value="excel_tables"> |
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7
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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)" />--> |
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76 <expand macro="checklist_input_macro"/> |
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77 <param name="xlsx_file" type="data" format="xlsx" label="Select Excel (xlsx) file based on template" /> |
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78 <expand macro="run_inputs_macro" /> |
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79 </when> |
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80 <when value="user_generated_tables"> |
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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)" />--> |
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82 <expand macro="checklist_input_macro"/> |
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1
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83 <expand macro="run_inputs_macro" /> |
|
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84 <param name="studies_users_table" type="data" format="tabular" multiple="false" label="Studies table" help="Studies metadata file"/> |
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85 <param name="samples_users_table" type="data" format="tabular" multiple="false" label="Samples table" help="Samples metadata file"/> |
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86 <param name="experiments_users_table" type="data" format="tabular" multiple="false" label="Experiments table" help="Experiments metadata file"/> |
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87 <param name="runs_users_table" type="data" format="tabular" multiple="false" label="Runs table" help="Runs metadata file"/> |
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88 </when> |
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89 <when value="build_tables"> |
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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?"/> |
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91 <conditional name="conditional_viral_metadata"> |
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92 <param name="viral_sample" type="boolean" truevalue="true" falsevalue="false" label="Does your submission contains viral samples?" /> |
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93 <when value="true"> |
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94 <expand macro="viral_samples" /> |
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95 </when> |
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96 <when value="false"> |
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97 <expand macro="nonviral_samples" /> |
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98 </when> |
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99 </conditional> |
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100 </when> |
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101 </conditional> |
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102 <param name="center" type="text" optional="False" label="Affiliation center"/> |
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103 </xml> |
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104 <xml name="viral_samples"> |
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105 <repeat name="rep_study" title="Study" min="1"> |
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106 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> |
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107 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> |
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108 <param name="study_type" type="select" label="Please select the type of study"> |
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109 <options from_data_table="study_type"> |
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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="study_pubmed_id" type="text" optional="True" value="" label="Please provide the PubMed id if exists (or leave it blank)"/> |
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114 <repeat name="rep_sample" title="Samples associated with this study" min="1" > |
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115 <param name="sample_title" type="text" label="Sample title"/> |
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116 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> |
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117 <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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118 <param name="tax_id" type="text" label="Enter the taxonomic ID corresponding to the sample species" /> |
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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"> |
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120 <option value="not collected">not collected</option> |
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121 <option value="restricted access">restricted access</option> |
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122 <option value="not provided">not provided</option> |
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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> |
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0
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124 </param> |
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125 <param name="geo_location_country" type="select" label="Select the country where the sample was obtained"> |
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126 <options from_data_table="geographic_location_1"> |
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127 <column name="value" index="0"/> |
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128 </options> |
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129 </param> |
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130 <param name="host_common_name" type="text" label="Host common name" help="e.g human"/> |
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131 <param name="host_subject_id" type="text" label="Host subject id"/> |
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132 <param name="host_health_state" type="select" label="Host health state"> |
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133 <options from_data_table="host_health_state_1"> |
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134 <column name="value" index="0"/> |
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135 </options> |
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136 </param> |
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137 <param name="host_sex" type="select" label="Host sex"> |
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138 <options from_data_table="host_sex_1"> |
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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 <param name="host_scientific_name" type="text" label="Host scientific name" help="e.g Homo sapiens"/> |
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143 <param name="collector_name" type="text" label="Collector name" help="Leave blank if unknown"/> |
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144 <param name="collecting_institution" type="text" label="Collecting institution"/> |
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145 <param name="isolate" type="text" label="Isolate"/> |
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146 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > |
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147 <param name="experiment_title" type="text" label="Specify an experiment title" /> |
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148 <param name="experiment_design" type="text" label="Describe the experiment design" /> |
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149 <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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150 <options from_data_table="library_strategy"> |
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151 <column name="value" index="0"/> |
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152 </options> |
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153 </param> |
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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"> |
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155 <options from_data_table="library_source"> |
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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="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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160 <options from_data_table="library_selection"> |
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161 <column name="value" index="0"/> |
|
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162 </options> |
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163 </param> |
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164 <param name="library_layout" type="select" label="Library layout"> |
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165 <options from_data_table="library_layout"> |
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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="insert_size" type="integer" value="0" label="Specify the insert size"/> |
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170 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> |
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171 <param name="platform" type="select" label="Select the sequencing platform used"> |
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172 <option value="LS454">LS454</option> |
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173 <option value="ILLUMINA">Illumina</option> |
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174 <option value="HELICOS">Helicos</option> |
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175 <option value="ABI_SOLID">ABI Solid</option> |
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176 <option value="COMPLETE_GENOMICS">Complete Genomics</option> |
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177 <option value="BGISEQ">BGI Seq</option> |
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178 <option value="OXFORD_NANOPORE">Oxford Nanopore</option> |
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179 <option value="PACBIO_SMRT">PacBio</option> |
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180 <option value="ION_TORRENT">Ion Torrent</option> |
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181 <option value="CAPILLARY">Capillary sequencing</option> |
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182 </param> |
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183 <param name="instrument_model" type="select" label="Instrument model"> |
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184 <options from_data_table="instrument_model"> |
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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 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > |
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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"/> |
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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"/> |
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191 </repeat> |
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192 </repeat> |
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193 </repeat> |
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194 </repeat> |
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195 </xml> |
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196 <xml name="nonviral_samples"> |
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197 <repeat name="rep_study" title="Study" min="1"> |
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198 <param name="study_title" type="text" optional="False" label="Please provide a short descriptive title for the study"/> |
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199 <param name="study_abstract" type="text" optional="True" label="Please provide an abstract to describe the study in detail"/> |
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200 <param name="study_type" type="select" label="Please select the type of study"> |
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201 <options from_data_table="study_type"> |
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202 <column name="value" index="0"/> |
|
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203 </options> |
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204 </param> |
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205 <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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206 <repeat name="rep_sample" title="Samples associated with this study" min="1" > |
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207 <param name="sample_title" type="text" label="Sample title"/> |
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208 <param name="sample_description" type="text" help="e.g: liver cells" label="Describe the type of sample"/> |
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209 <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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210 <param name="tax_id" type="integer" value="0" label="Enter the taxonomic ID corresponding to the sample species" /> |
|
0
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211 <repeat name="rep_experiment" title="Sequencing experiments performed with this sample" min="1" > |
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212 <param name="experiment_title" type="text" label="Specify an experiment title" /> |
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213 <param name="experiment_design" type="text" label="Describe the experiment design" /> |
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214 <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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215 <options from_data_table="library_strategy"> |
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216 <column name="value" index="0"/> |
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217 </options> |
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218 </param> |
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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"> |
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220 <options from_data_table="library_source"> |
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221 <column name="value" index="0"/> |
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222 </options> |
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223 </param> |
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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"> |
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225 <options from_data_table="library_selection"> |
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226 <column name="value" index="0"/> |
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227 </options> |
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228 </param> |
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229 <param name="library_layout" type="select" label="Library layout"> |
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230 <options from_data_table="library_layout"> |
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231 <column name="value" index="0"/> |
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232 </options> |
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233 </param> |
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234 <param name="insert_size" type="integer" value="0" label="Specify the insert size"/> |
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235 <param name="library_construction_protocol" type="text" label="Please describe the library construction protocol"/> |
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236 <param name="platform" type="select" label="Select the sequencing platform used"> |
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237 <option value="LS454">LS454</option> |
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1
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238 <option value="ILLUMINA" selected="True">Illumina</option> |
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0
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239 <option value="HELICOS">Helicos</option> |
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240 <option value="ABI_SOLID">ABI Solid</option> |
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241 <option value="COMPLETE_GENOMICS">Complete Genomics</option> |
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242 <option value="BGISEQ">BGI Seq</option> |
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243 <option value="OXFORD_NANOPORE">Oxford Nanopore</option> |
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244 <option value="PACBIO_SMRT">PacBio</option> |
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245 <option value="ION_TORRENT">Ion Torrent</option> |
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246 <option value="CAPILLARY">Capillary sequencing</option> |
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247 </param> |
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248 <param name="instrument_model" type="select" label="Instrument model"> |
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249 <options from_data_table="instrument_model"> |
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250 <column name="value" index="0"/> |
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251 </options> |
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252 </param> |
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253 <repeat name="rep_runs" title="Runs executed within this experiment" min="1" > |
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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"/> |
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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"/> |
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256 </repeat> |
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257 </repeat> |
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258 </repeat> |
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259 </repeat> |
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260 </xml> |
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261 </macros> |