Mercurial > repos > iuc > snpeff
annotate snpEff_download.xml @ 3:b24873564cf6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author | iuc |
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date | Tue, 07 Jun 2016 10:03:17 -0400 |
parents | 500832f27cbc |
children | 698ef30638a8 |
rev | line source |
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1 | 1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0"> |
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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6 <expand macro="requirements" /> |
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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7 <expand macro="stdio" /> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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1
diff
changeset
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8 <expand macro="version_command" /> |
0 | 9 <command> |
1 | 10 <![CDATA[ |
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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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11 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version" |
1 | 12 ]]> |
0 | 13 </command> |
14 <inputs> | |
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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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15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> |
1 | 16 <help>@SNPEFF_DATABASE_URL@</help> |
17 <validator type="regex" message="A genome version name is required">\S+</validator> | |
0 | 18 </param> |
19 </inputs> | |
20 <outputs> | |
1 | 21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> |
0 | 22 </outputs> |
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b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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diff
changeset
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23 <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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24 <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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25 <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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26 <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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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 <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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29 </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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30 </output> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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diff
changeset
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31 </test> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
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diff
changeset
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32 </tests> |
b24873564cf6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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1
diff
changeset
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33 <help><![CDATA[ |
0 | 34 |
35 @EXTERNAL_DOCUMENTATION@ | |
36 | |
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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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37 ]]> |
0 | 38 </help> |
1 | 39 <expand macro="citations" /> |
0 | 40 </tool> |
41 |