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comparison macros.xml @ 4:9a5be5b1a5c9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
author iuc
date Wed, 04 Dec 2019 06:51:08 -0500
parents 9bdcba262627
children 8cebdc74a48f
comparison
equal deleted inserted replaced
3:9bdcba262627 4:9a5be5b1a5c9
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@WRAPPER_VERSION@">1.2.3</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
21 <xml name="citations"> 21 <xml name="citations">
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 <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> 26 <!-- See the kraken_databases.loc.sample documentation,
27 <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> 27 this if statement is for backward compatibility as early
28 versions of the wrapper assumed the UI facing field name
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>
31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
28 </macros> 32 </macros>