Mercurial > repos > devteam > kraken
annotate macros.xml @ 9:aec58624706f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
author | iuc |
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date | Wed, 04 Dec 2019 06:51:45 -0500 |
parents | 8ba2174315aa |
children | 766d5f63b0f4 |
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0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <?xml version="1.0"?> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 <macros> |
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aec58624706f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
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3 <token name="@WRAPPER_VERSION@">1.3.1</token> |
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0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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4 <xml name="requirements"> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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5 <requirements> |
9
aec58624706f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
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6 <requirement type="package" version="1.1.1">kraken</requirement> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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7 </requirements> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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8 </xml> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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9 <xml name="version_command"> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
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10 <version_command><![CDATA[ |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
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11 export LC_ALL=C && kraken --version |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
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12 ]]></version_command> |
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0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
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13 </xml> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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14 <xml name="input_database"> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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15 <param label="Select a Kraken database" name="kraken_database" type="select"> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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16 <options from_data_table="kraken_databases"> |
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2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
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17 <validator message="No Kraken database is available" type="no_options" /> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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18 </options> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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19 </param> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 </xml> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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21 <xml name="citations"> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 <citations> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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23 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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24 </citations> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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25 </xml> |
8
8ba2174315aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
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26 <!-- See the kraken_databases.loc.sample documentation, |
9
aec58624706f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents:
8
diff
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27 this if statement is for backward compatibility as early |
aec58624706f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents:
8
diff
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28 versions of the wrapper assumed the UI facing field name |
aec58624706f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents:
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29 was also part of the directory path --> |
8
8ba2174315aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
parents:
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30 <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token> |
8ba2174315aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
iuc
parents:
7
diff
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31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
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32 </macros> |