Mercurial > repos > bgruening > pg_query

annotate macros.xml @ 0:fa1a61331039 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
author bgruening
date Wed, 24 Apr 2019 06:12:05 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
1 <?xml version="1.0"?>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
2 <macros>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
3 <xml name="inputs_outputs">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
4 <inputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
5 <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
6 <yield />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
7 </inputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
8 <outputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
9 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" />
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
10 </outputs>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
11 </xml>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
12
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
13 <xml name="requirements">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
14 <requirements>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
15 <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
16 <requirement type="package" version="0.1">pglite</requirement>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
17 </requirements>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
18 </xml>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
19
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
20 <token name="@PG_VERSION@">11.2</token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
21
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
22 <token name="@HELP_FOOTER@">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
23 The postgresql tools, are using a postgresql database in user-space. Databases are packed into a tarball and stored in the user-history.
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
24 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
25
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
26 <token name="@UNTAR_INFILE@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
27 tar -xjvf '$infile' &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
28 export PWD=`pwd` &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
29 sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '\$PWD/postgresql/'|" ./postgresql/db/postgresql.conf
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
30 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
31 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
32
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
33 <token name="@PG_SETUP@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
34 pglite setup -d ./postgresql &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
35 @PG_START@
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
36 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
37 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
38
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
39 <token name="@PSQL@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
40 psql "\$(pglite url -d ./postgresql)"
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
41 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
42 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
43
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
44 <token name="@STATUS_RUNNING@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
45 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
46 pglite status -d ./postgresql &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
47 timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done'
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
48 && pglite status -d ./postgresql
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
49 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
50 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
51
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
52 <token name="@STOPPED@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
53 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
54 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
55 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
56
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
57 <token name="@PG_START@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
58 pglite start -d ./postgresql &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
59 @STATUS_RUNNING@
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
60 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
61 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
62
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
63 <token name="@PG_STOP@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
64 pglite stop -d ./postgresql &&
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
65 @STOPPED@
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
66 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
67 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
68
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
69 <token name="@ARCHIVE_DATABASE@"><![CDATA[
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
70 tar -cvjf postgresql_out.tar.bz2 postgresql
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
71 ]]>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
72 </token>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
73 <xml name="citations">
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
74 <citations></citations>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
75 </xml>
fa1a61331039 planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
bgruening
parents:
diff changeset
76 </macros>