Mercurial > repos > iuc > data_manager_gemini_database_downloader
annotate data_manager/data_manager_gemini_download.xml @ 9:27a6a256cd23 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
author | iuc |
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date | Sat, 03 Dec 2022 10:37:24 +0000 |
parents | f57426daa04d |
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27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
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1 <tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@+galaxy1" tool_type="manage_data" profile="18.09"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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2 <description>the annotation files required by the GEMINI suite of tools</description> |
fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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3 <macros> |
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f57426daa04d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 62ed732cba355e695181924a8ed4cce49ca21c59
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4 <token name="@VERSION@">0.20.1</token> |
f57426daa04d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 62ed732cba355e695181924a8ed4cce49ca21c59
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5 <token name="@DB_VERSION@">200</token> |
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fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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6 </macros> |
0 | 7 <requirements> |
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fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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8 <requirement type="package" version="@VERSION@">gemini</requirement> |
0 | 9 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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10 <command detect_errors="exit_code"> |
172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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11 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file' |
0 | 12 </command> |
13 <inputs> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
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14 <param name="cadd" type="boolean" truevalue="cadd" falsevalue="" checked="True" |
0 | 15 label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/> |
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27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
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16 <param name="gerp_bp" type="boolean" truevalue="gerp_bp" falsevalue="" checked="True" |
0 | 17 label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> |
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fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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18 <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/> |
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27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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19 <param name="test_data_manager" type="hidden" value=""/> |
0 | 20 </inputs> |
21 <outputs> | |
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172815da3d41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
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22 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
0 | 23 </outputs> |
24 <tests> | |
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27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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25 <test expect_num_outputs="1"> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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26 <param name="test_data_manager" value="--test" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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27 <param name="cadd" value="false" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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28 <param name="gerp_bp" value="false" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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29 <output name="out_file" file="test.json" compare="re_match" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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30 </test> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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31 <!-- Test 2 with the latest option --> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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diff
changeset
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32 <test expect_num_outputs="1"> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
parents:
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diff
changeset
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33 <param name="test_data_manager" value="--test" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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changeset
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34 <output name="out_file"> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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35 <assert_contents> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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36 <has_text text=""name": "GEMINI annotations w/ GERP & CADD" /> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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changeset
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37 </assert_contents> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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changeset
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38 </output> |
27a6a256cd23
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d
iuc
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changeset
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39 </test> |
0 | 40 </tests> |
41 <help> | |
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fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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42 This tool downloads the GEMINI annotation files and makes them available to |
fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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43 corresponding versions of the GEMINI suite of tools. Downloading the (very large) CADD_ scores and GERP_ annotation files is optional. |
0 | 44 |
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fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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45 Please visit http://gemini.readthedocs.io for details about GEMINI. |
fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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46 |
fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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47 .. _GERP: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html |
fe5a9a7d95b0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 283362494058ed64143b1f27afb447b8a1cb4313
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48 .. _CADD: https://cadd.gs.washington.edu/ |
0 | 49 </help> |
50 <citations> | |
51 <citation type="doi">10.1371/journal.pcbi.1003153</citation> | |
52 </citations> | |
53 </tool> | |
54 |