Mercurial > repos > devteam > kraken
comparison 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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8:8ba2174315aa | 9:aec58624706f |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@WRAPPER_VERSION@">1.3.0</token> | 3 <token name="@WRAPPER_VERSION@">1.3.1</token> |
4 <xml name="requirements"> | 4 <xml name="requirements"> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> | 6 <requirement type="package" version="1.1.1">kraken</requirement> |
7 </requirements> | 7 </requirements> |
8 </xml> | 8 </xml> |
9 <xml name="version_command"> | 9 <xml name="version_command"> |
10 <version_command><![CDATA[ | 10 <version_command><![CDATA[ |
11 export LC_ALL=C && kraken --version | 11 export LC_ALL=C && kraken --version |
22 <citations> | 22 <citations> |
23 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | 23 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> |
24 </citations> | 24 </citations> |
25 </xml> | 25 </xml> |
26 <!-- See the kraken_databases.loc.sample documentation, | 26 <!-- See the kraken_databases.loc.sample documentation, |
27 this if statement is for backward compatibility as early | 27 this if statement is for backward compatibility as early |
28 versions of the wrapper assumed the UI facing field name | 28 versions of the wrapper assumed the UI facing field name |
29 was also part of the directory path --> | 29 was also part of the directory path --> |
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='${kraken_database.fields.path}'; fi</token> | 30 <token name="@SET_DATABASE_PATH@">if [ -d '${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> |
31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> | 31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> |
32 </macros> | 32 </macros> |