Mercurial > repos > gga > chado_organism_delete_organisms

annotate macros.xml @ 18:36777878aabb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 170209d14cabe6ce8ab7b9f06df7fbf36af2ba43"
author gga
date Tue, 04 May 2021 12:52:50 +0000
parents 618a26fbb5a0
children 49df24f153f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
1 <?xml version="1.0"?>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
2 <macros>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
3 <xml name="requirements">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
4 <requirements>
12
80dc4a25db97 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
gga
parents: 11
diff changeset
5 <requirement type="package" version="@LIB_VERSION@">python-chado</requirement>
1
5b0a84b6672d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 53d8f1212a5602a4692517c44e0285228087e3f2
gga
parents: 0
diff changeset
6 <requirement type="package" version="1.5">jq</requirement>
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
7 <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
8 <requirement type="package" version="0.1">pglite</requirement>
0
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
9 <yield/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
10 </requirements>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
11 </xml>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
12
18
36777878aabb "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 170209d14cabe6ce8ab7b9f06df7fbf36af2ba43"
gga
parents: 17
diff changeset
13 <token name="@LIB_VERSION@">2.3.6</token>
16
b1aa4f9d82fe "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0a8b62b6cdce301067cba25d30171d5f6ec04f40"
gga
parents: 15
diff changeset
14 <token name="@WRAPPER_VERSION@">@LIB_VERSION@+galaxy0</token>
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
15 <token name="@PG_VERSION@">11.2</token>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
16
0
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
17 <xml name="stdio">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
18 <stdio>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
19 <regex level="fatal" match="Exception:" source="stderr" />
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
20 <regex level="fatal" match="error" source="stderr" />
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
21 <exit_code range="1:" />
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
22 </stdio>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
23 </xml>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
24
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
25 <xml name="citation">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
26 <citations>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
27 </citations>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
28 </xml>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
29
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
30 <token name="@HELP_OVERVIEW@"><![CDATA[
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
31 **Python-chado Overview**
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
32
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
33 Python-cado provides several tools allowing to load data into a remote Chado database.
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
34 ]]></token>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
35
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
36 <token name="@HELP@"><![CDATA[
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
37 ]]></token>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
38
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
39 <xml name="sanitized">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
40 <sanitizer>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
41 <valid initial="string.printable">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
42 <remove value="&apos;"/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
43 </valid>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
44 <mapping initial="none">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
45 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
46 <add source="(" target="\("/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
47 <add source=")" target="\)"/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
48 </mapping>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
49 </sanitizer>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
50 </xml>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
51
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
52 <!-- I'm not proud of it, but it is needed for workflows -->
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
53 <xml name="wait_for">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
54 <param name="wait_for"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
55 type="data"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
56 format="data"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
57 optional="true"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
58 label="Run this only after the following dataset is ready"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
59 help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
60 </xml>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
61
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
62 <xml name="feature_rel">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
63 <param name="rel_subject_re"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
64 argument="--rel-subject-re"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
65 type="text"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
66 label="Regular expression to extract the unique name of the parent feature"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
67 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
68 <expand macro="sanitized"/>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
69 </param>
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
70
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
71 <param name="rel_subject_type"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
72 argument="--rel-subject-type"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
73 type="text"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
74 label="Sequence type of the parent"
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
75 help="this should be a Sequence Ontology term" />
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
76 </xml>
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
77
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
78 <xml name="psql_target">
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
79 <conditional name="psql_target">
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
80 <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables">
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
81 <option value="remote">Remote database</option>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
82 <option value="pgtools">Database from history</option>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
83 </param>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
84 <when value="remote"/>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
85 <when value="pgtools">
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
86 <param name="infile" type="data" format="postgresql" label="Input database" />
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
88 </when>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
89 </conditional>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
90 </xml>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
91
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
92 <token name="@START_PSQL@"><![CDATA[
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
93 #if $psql_target.method == 'pgtools'
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
94 tar -xjvf '$psql_target.infile' > /dev/null &&
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
95 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
96 #else
11
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
97 if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
98 echo "__default: local" > '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
99 echo "local:" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
100 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
101 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
102 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
103 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
104 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
105 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
106
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
107 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
108 ; fi
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
109 #end if
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
110 ]]></token>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
111
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
112 <token name="@STOP_PSQL@"><![CDATA[
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
113 #if $psql_target.method == 'pgtools'
11
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
114 &&
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
115 pglite stop -d ./postgresql &&
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
116 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
117 ;
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
118 ## Make sure psql is stopped even if loading script failed
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
119 pglite stop -d ./postgresql || true
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
120 #end if
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
121 ]]></token>
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
122
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
123 <token name="@ZIP_PSQL@"><![CDATA[
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
124 #if $psql_target.method == 'pgtools'
11
c09cee3486a4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
gga
parents: 10
diff changeset
125 &&
10
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
126 pglite stop -d ./postgresql &&
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
127 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
128 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
129 ;
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
130 ## Make sure psql is stopped even if loading script failed
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
131 pglite stop -d ./postgresql || true
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
132 #end if
87df7adce77e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
parents: 8
diff changeset
133 ]]></token>
0
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
134 </macros>