Mercurial > repos > iuc > snpeff
annotate snpEff_download.xml @ 9:68693743661e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit dd7c0bd39f1f70fca81c1a5e25e71495aed231d9
author | iuc |
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date | Tue, 14 Nov 2017 05:42:51 -0500 |
parents | 7adfd0589f49 |
children | 5b4ac70948d2 |
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9
68693743661e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit dd7c0bd39f1f70fca81c1a5e25e71495aed231d9
iuc
parents:
7
diff
changeset
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1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.1"> |
0 | 2 <description>Download a new database</description> |
3 <macros> | |
4 <import>snpEff_macros.xml</import> | |
5 </macros> | |
3
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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1
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changeset
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6 <expand macro="requirements" /> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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7 <expand macro="stdio" /> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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8 <expand macro="version_command" /> |
7
7adfd0589f49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents:
4
diff
changeset
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9 <command><![CDATA[ |
7adfd0589f49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents:
4
diff
changeset
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10 snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version' |
7adfd0589f49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents:
4
diff
changeset
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11 ]]></command> |
0 | 12 <inputs> |
7
7adfd0589f49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents:
4
diff
changeset
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13 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)"> |
1 | 14 <help>@SNPEFF_DATABASE_URL@</help> |
15 <validator type="regex" message="A genome version name is required">\S+</validator> | |
0 | 16 </param> |
17 </inputs> | |
18 <outputs> | |
1 | 19 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> |
0 | 20 </outputs> |
3
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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21 <tests> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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22 <test> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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23 <param name="genome_version" value="ebola_zaire"/> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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24 <output name="snpeff_db"> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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25 <assert_contents> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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26 <has_text text="ebola_zaire" /> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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27 </assert_contents> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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28 </output> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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29 </test> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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30 </tests> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
1
diff
changeset
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31 <help><![CDATA[ |
0 | 32 @EXTERNAL_DOCUMENTATION@ |
7
7adfd0589f49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
iuc
parents:
4
diff
changeset
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33 ]]></help> |
1 | 34 <expand macro="citations" /> |
0 | 35 </tool> |