Mercurial > repos > gga > chado_expression_delete_biomaterials
comparison macros.xml @ 5:9e40ea0d1530 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author | gga |
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date | Mon, 08 Jul 2019 05:37:25 -0400 |
parents | 803dcdcedbf8 |
children | 79d117de8e30 |
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4:769bcd006045 | 5:9e40ea0d1530 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <xml name="requirements"> | 3 <xml name="requirements"> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2.2.5">python-chado</requirement> | 5 <requirement type="package" version="2.2.6">python-chado</requirement> |
6 <requirement type="package" version="1.5">jq</requirement> | 6 <requirement type="package" version="1.5">jq</requirement> |
7 <requirement type="package" version="@PG_VERSION@">postgresql</requirement> | |
8 <requirement type="package" version="0.1">pglite</requirement> | |
7 <yield/> | 9 <yield/> |
8 </requirements> | 10 </requirements> |
9 </xml> | 11 </xml> |
12 | |
13 <token name="@PG_VERSION@">11.2</token> | |
10 | 14 |
11 <xml name="stdio"> | 15 <xml name="stdio"> |
12 <stdio> | 16 <stdio> |
13 <regex level="fatal" match="Exception:" source="stderr" /> | 17 <regex level="fatal" match="Exception:" source="stderr" /> |
14 <regex level="fatal" match="error" source="stderr" /> | 18 <regex level="fatal" match="error" source="stderr" /> |
15 <exit_code range="1:" /> | 19 <exit_code range="1:" /> |
16 </stdio> | 20 </stdio> |
17 </xml> | 21 </xml> |
18 | 22 |
19 <token name="@WRAPPER_VERSION@">2.2.5</token> | 23 <token name="@WRAPPER_VERSION@">2.2.6</token> |
20 | 24 |
21 <xml name="citation"> | 25 <xml name="citation"> |
22 <citations> | 26 <citations> |
23 </citations> | 27 </citations> |
24 </xml> | 28 </xml> |
28 | 32 |
29 Python-cado provides several tools allowing to load data into a remote Chado database. | 33 Python-cado provides several tools allowing to load data into a remote Chado database. |
30 ]]></token> | 34 ]]></token> |
31 | 35 |
32 <token name="@HELP@"><![CDATA[ | 36 <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> | 37 ]]></token> |
47 | 38 |
48 <xml name="sanitized"> | 39 <xml name="sanitized"> |
49 <sanitizer> | 40 <sanitizer> |
50 <valid initial="string.printable"> | 41 <valid initial="string.printable"> |
81 argument="--rel-subject-type" | 72 argument="--rel-subject-type" |
82 type="text" | 73 type="text" |
83 label="Sequence type of the parent" | 74 label="Sequence type of the parent" |
84 help="this should be a Sequence Ontology term" /> | 75 help="this should be a Sequence Ontology term" /> |
85 </xml> | 76 </xml> |
77 | |
78 <xml name="psql_target"> | |
79 <conditional name="psql_target"> | |
80 <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables"> | |
81 <option value="remote">Remote database</option> | |
82 <option value="pgtools">Database from history</option> | |
83 </param> | |
84 <when value="remote"/> | |
85 <when value="pgtools"> | |
86 <param name="infile" type="data" format="postgresql" label="Input database" /> | |
87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/> | |
88 </when> | |
89 </conditional> | |
90 </xml> | |
91 | |
92 <token name="@AUTH@"><![CDATA[ | |
93 if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then | |
94 echo "__default: local" > '.auth.yml' && | |
95 echo "local:" >> '.auth.yml' && | |
96 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' && | |
97 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' && | |
98 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' && | |
99 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' && | |
100 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' && | |
101 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' && | |
102 | |
103 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml' | |
104 ; fi | |
105 ]]></token> | |
106 | |
107 <token name="@START_PSQL@"><![CDATA[ | |
108 #if $psql_target.method == 'pgtools' | |
109 tar -xjvf '$psql_target.infile' > /dev/null && | |
110 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema' | |
111 #else | |
112 @AUTH@ | |
113 #end if | |
114 ]]></token> | |
115 | |
116 <token name="@STOP_PSQL@"><![CDATA[ | |
117 #if $psql_target.method == 'pgtools' | |
118 pglite stop -d ./postgresql && | |
119 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' | |
120 ; | |
121 ## Make sure psql is stopped even if loading script failed | |
122 pglite stop -d ./postgresql || true | |
123 #end if | |
124 ]]></token> | |
125 | |
126 <token name="@ZIP_PSQL@"><![CDATA[ | |
127 #if $psql_target.method == 'pgtools' | |
128 pglite stop -d ./postgresql && | |
129 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' && | |
130 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null | |
131 ; | |
132 ## Make sure psql is stopped even if loading script failed | |
133 pglite stop -d ./postgresql || true | |
134 #end if | |
135 ]]></token> | |
86 </macros> | 136 </macros> |