Mercurial > repos > iuc > data_manager_gemini_database_downloader

annotate data_manager/data_manager_gemini_download.xml @ 9:27a6a256cd23 draft default tip

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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
author iuc
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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2 <description>the annotation files required by the GEMINI suite of tools</description>
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3 <macros>
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4 <token name="@VERSION@">0.20.1</token>
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5 <token name="@DB_VERSION@">200</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">gemini</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
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12 </command>
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13 <inputs>
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14 <param name="cadd" type="boolean" truevalue="cadd" falsevalue="" checked="True"
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15 label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
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16 <param name="gerp_bp" type="boolean" truevalue="gerp_bp" falsevalue="" checked="True"
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17 label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
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18 <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/>
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19 <param name="test_data_manager" type="hidden" value=""/>
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20 </inputs>
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21 <outputs>
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22 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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23 </outputs>
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24 <tests>
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25 <test expect_num_outputs="1">
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26 <param name="test_data_manager" value="--test" />
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27 <param name="cadd" value="false" />
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28 <param name="gerp_bp" value="false" />
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29 <output name="out_file" file="test.json" compare="re_match" />
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30 </test>
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31 <!-- Test 2 with the latest option -->
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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
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33 <param name="test_data_manager" value="--test" />
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34 <output name="out_file">
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35 <assert_contents>
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36 <has_text text="&quot;name&quot;: &quot;GEMINI annotations w/ GERP &amp; CADD" />
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37 </assert_contents>
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38 </output>
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39 </test>
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40 </tests>
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41 <help>
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42 This tool downloads the GEMINI annotation files and makes them available to
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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.
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44
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45 Please visit http://gemini.readthedocs.io for details about GEMINI.
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47 .. _GERP: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html
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48 .. _CADD: https://cadd.gs.washington.edu/
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49 </help>
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50 <citations>
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51 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
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52 </citations>
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53 </tool>
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54