Mercurial > repos > gga > chado_expression_add_expression

comparison macros.xml @ 0:c09e35ef9d09 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
author gga
date Mon, 05 Nov 2018 08:04:56 -0500
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children 0214383c6578
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-1:000000000000 0:c09e35ef9d09
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="2.2.2">python-chado</requirement>
6 <requirement type="package" version="1.5">jq</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10
11 <xml name="stdio">
12 <stdio>
13 <regex level="fatal" match="Exception:" source="stderr" />
14 <regex level="fatal" match="error" source="stderr" />
15 <exit_code range="1:" />
16 </stdio>
17 </xml>
18
19 <token name="@WRAPPER_VERSION@">2.1.5</token>
20
21 <xml name="citation">
22 <citations>
23 </citations>
24 </xml>
25
26 <token name="@HELP_OVERVIEW@"><![CDATA[
27 **Python-chado Overview**
28
29 Python-cado provides several tools allowing to load data into a remote Chado database.
30 ]]></token>
31
32 <token name="@HELP@"><![CDATA[
33 ]]></token>
34
35 <token name="@AUTH@"><![CDATA[
36 echo "__default: local" > '.auth.yml' &&
37 echo "local:" >> '.auth.yml' &&
38 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
39 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
40 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
41 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
42 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
43 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
44
45 CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
46 ]]></token>
47
48 <xml name="sanitized">
49 <sanitizer>
50 <valid initial="string.printable">
51 <remove value="&apos;"/>
52 </valid>
53 <mapping initial="none">
54 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
55 <add source="(" target="\("/>
56 <add source=")" target="\)"/>
57 </mapping>
58 </sanitizer>
59 </xml>
60
61 <!-- I'm not proud of it, but it is needed for workflows -->
62 <xml name="wait_for">
63 <param name="wait_for"
64 type="data"
65 format="data"
66 optional="true"
67 label="Run this only after the following dataset is ready"
68 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."/>
69 </xml>
70
71 <xml name="feature_rel">
72 <param name="rel_subject_re"
73 argument="--rel-subject-re"
74 type="text"
75 label="Regular expression to extract the unique name of the parent feature"
76 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
77 <expand macro="sanitized"/>
78 </param>
79
80 <param name="rel_subject_type"
81 argument="--rel-subject-type"
82 type="text"
83 label="Sequence type of the parent"
84 help="this should be a Sequence Ontology term" />
85 </xml>
86 </macros>