Mercurial > repos > devteam > kraken_filter

annotate macros.xml @ 4:3d6570bffdb1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
author iuc
date Wed, 04 Dec 2019 06:51:27 -0500
parents 5bee9adae474
children 67236d921e83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
2 <macros>
4
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
3 <token name="@WRAPPER_VERSION@">1.3.1</token>
0
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
4 <xml name="requirements">
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
5 <requirements>
4
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
6 <requirement type="package" version="1.1.1">kraken</requirement>
0
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
7 </requirements>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
8 </xml>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
9 <xml name="version_command">
3
5bee9adae474 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents: 2
diff changeset
10 <version_command><![CDATA[
5bee9adae474 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents: 2
diff changeset
11 export LC_ALL=C && kraken --version
5bee9adae474 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents: 2
diff changeset
12 ]]></version_command>
0
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
13 </xml>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
14 <xml name="input_database">
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
15 <param label="Select a Kraken database" name="kraken_database" type="select">
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
16 <options from_data_table="kraken_databases">
3
5bee9adae474 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents: 2
diff changeset
17 <validator message="No Kraken database is available" type="no_options" />
0
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
18 </options>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
19 </param>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
20 </xml>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
21 <xml name="citations">
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
22 <citations>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
23 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
24 </citations>
cbb802a726fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff changeset
25 </xml>
4
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
26 <!-- See the kraken_databases.loc.sample documentation,
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
27 this if statement is for backward compatibility as early
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
28 versions of the wrapper assumed the UI facing field name
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
29 was also part of the directory path -->
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
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>
3d6570bffdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
parents: 3
diff changeset
31 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
3
5bee9adae474 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents: 2
diff changeset
32 </macros>