Mercurial > repos > gga > chado_expression_add_biomaterial
comparison macros.xml @ 0:676c49ac9cb5 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
author | gga |
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date | Mon, 05 Nov 2018 08:10:25 -0500 |
parents | |
children | e60fc2879221 |
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-1:000000000000 | 0:676c49ac9cb5 |
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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="'"/> | |
52 </valid> | |
53 <mapping initial="none"> | |
54 <add source="'" target="'"'"'"/> | |
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> |