Mercurial > repos > gga > chado_feature_load_gff

comparison macros.xml @ 0:04f12e56d4c7 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:45:47 -0400
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children 7af45fc803fd
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-1:000000000000 0:04f12e56d4c7
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="2.1.2">python-chado</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9
10 <xml name="stdio">
11 <stdio>
12 <regex level="fatal" match="Exception:" source="stderr" />
13 <regex level="fatal" match="error" source="stderr" />
14 <exit_code range="1:" />
15 </stdio>
16 </xml>
17
18 <token name="@WRAPPER_VERSION@">2.1.1</token>
19
20 <xml name="citation">
21 <citations>
22 </citations>
23 </xml>
24
25 <token name="@HELP_OVERVIEW@"><![CDATA[
26 **Python-chado Overview**
27
28 Python-cado provides several tools allowing to load data into a remote Chado database.
29 ]]></token>
30
31 <token name="@HELP@"><![CDATA[
32 ]]></token>
33
34 <token name="@AUTH@"><![CDATA[
35 echo "__default: local" > '.auth.yml' &&
36 echo "local:" >> '.auth.yml' &&
37 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
38 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
39 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
40 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
41 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
42 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
43
44 CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
45 ]]></token>
46
47 <xml name="sanitized">
48 <sanitizer>
49 <valid initial="string.printable">
50 <remove value="&apos;"/>
51 </valid>
52 <mapping initial="none">
53 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
54 <add source="(" target="\("/>
55 <add source=")" target="\)"/>
56 </mapping>
57 </sanitizer>
58 </xml>
59
60 <!-- I'm not proud of it, but it is needed for workflows -->
61 <xml name="wait_for">
62 <param name="wait_for"
63 type="data"
64 format="data"
65 optional="true"
66 label="Run this only after the following dataset is ready"
67 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."/>
68 </xml>
69
70 <xml name="feature_rel">
71 <param name="rel_subject_re"
72 argument="--rel-subject-re"
73 type="text"
74 label="Regular expression to extract the unique name of the parent feature"
75 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
76 <expand macro="sanitized"/>
77 </param>
78
79 <param name="rel_subject_type"
80 argument="--rel-subject-type"
81 type="text"
82 label="Sequence type of the parent"
83 help="this should be a Sequence Ontology term" />
84 </xml>
85 </macros>