Mercurial > repos > gga > tripal_phylogeny_sync

comparison macros.xml @ 0:d1f5c6c38277 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1
author gga
date Mon, 06 Aug 2018 04:45:30 -0400
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children 159fd092ca62
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-1:000000000000 0:d1f5c6c38277
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="3.0">python-tripal</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@">3.0</token>
19
20 <xml name="citation">
21 <citations>
22 <citation type="doi">10.1093/database/bat075</citation>
23 </citations>
24 </xml>
25
26 <token name="@HELP_OVERVIEW@"><![CDATA[
27 **Python-tripal Overview**
28
29 Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database.
30 The tripal_rest_api Tripal module must be installed on the remote server to use these tools.
31 ]]></token>
32
33 <token name="@HELP@"><![CDATA[
34 **Useful Links**
35
36 `Tripal project website <http://tripal.info/>`_
37
38 `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools
39 ]]></token>
40
41 <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
42
43 <token name="@AUTH@"><![CDATA[
44 echo "__default: local" > '.auth.yml' &&
45 echo "local:" >> '.auth.yml' &&
46 echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
47 echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
48 echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
49
50 TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
51 ]]></token>
52
53 <xml name="wait_for">
54 <param name="wait_for"
55 type="data"
56 format="data"
57 optional="true"
58 label="Run this only after the following dataset is ready"
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."/>
60 </xml>
61
62 <xml name="test_result">
63 <assert_stderr>
64 <has_text text="MissingSchema" />
65 </assert_stderr>
66 </xml>
67
68 <xml name="analysis">
69 <section name="analysis" title="Analysis" expanded="True">
70 <param name="name"
71 type="text"
72 label="The analysis name [mandatory]">
73 <expand macro="sanitized"/>
74 </param>
75
76 <param name="program"
77 type="text"
78 label="Program name [mandatory]"
79 help="Name of the program that was used to perform this analysis">
80 <expand macro="sanitized"/>
81 </param>
82 <param name="program_version"
83 type="text"
84 label="Program version [mandatory]"
85 help="Version of the program that was used to perform this analysis"/>
86 <param name="source"
87 type="text"
88 label="Source name [mandatory]"
89 help="Where this analysis comes from">
90 <expand macro="sanitized"/>
91 </param>
92
93 <param name="source_version"
94 argument="--sourceversion"
95 type="text"
96 optional="True"
97 label="Source version" />
98 <param name="source_uri"
99 argument="--sourceuri"
100 type="text"
101 optional="True"
102 label="Source URI"
103 help="URI where source data was retrieved" />
104 <param name="algorithm"
105 argument="--algorithm"
106 type="text"
107 label="Algorithm"
108 optional="True"
109 help="Algorithm of the program that was used to perform this analysis" />
110 <param name="description"
111 argument="--description"
112 type="text"
113 optional="True"
114 label="Analysis description">
115 <expand macro="sanitized"/>
116 </param>
117 <param name="date"
118 argument="--date_executed"
119 type="text"
120 optional="True"
121 label="Execution date"
122 help="Format: yyyy-mm-dd Default: Today">
123 <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
124 </param>
125 </section>
126 </xml>
127
128 <xml name="feature_rel">
129 <param name="rel_subject_re"
130 argument="--rel-subject-re"
131 type="text"
132 label="Regular expression to extract the unique name of the parent feature"
133 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
134 <expand macro="sanitized"/>
135 </param>
136
137 <param name="rel_subject_type"
138 argument="--rel-subject-type"
139 type="text"
140 label="Sequence type of the parent"
141 help="this should be a Sequence Ontology term" />
142 </xml>
143
144 <xml name="match_type">
145 <param name="match_type"
146 argument="--match-type"
147 type="select"
148 label="Match type for already loaded features">
149 <option value="uniquename" selected="true">Unique name</option>
150 <option value="name">Name</option>
151 </param>
152 </xml>
153
154 <xml name="matching">
155 <section name="matching" title="Feature matching" expanded="True">
156 <param name="query_type"
157 type="text"
158 label="The feature type of the blast query"
159 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
160
161 <param name="query_uniquename"
162 type="boolean"
163 checked="false"
164 truevalue="--query_uniquename"
165 falsevalue=""
166 label="Find blast query features using their Unique name"
167 help="Feature name will be used otherwise" />
168
169 <param name="query_re"
170 type="text"
171 optional="true"
172 label="Regular expression to extract the feature name from the blast query name"
173 help="leave empty if the first word in query name is sufficient">
174 <expand macro="sanitized"/>
175 </param>
176 </section>
177 </xml>
178
179 <xml name="sanitized">
180 <sanitizer>
181 <valid initial="string.printable">
182 <remove value="&apos;"/>
183 </valid>
184 <mapping initial="none">
185 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
186 <add source="(" target="\("/>
187 <add source=")" target="\)"/>
188 </mapping>
189 </sanitizer>
190 </xml>
191
192 <token name="@MATCHING@"><![CDATA[
193 #if str($matching.query_re):
194 --query_re '${matching.query_re}'
195 #end if
196
197 $matching.query_uniquename
198
199 --query_type '$matching.query_type'
200 ]]></token>
201
202 <token name="@ANALYSIS@"><![CDATA[
203 #if $analysis.algorithm:
204 --algorithm '$analysis.algorithm'
205 #end if
206 #if $analysis.source_version:
207 --sourceversion '$analysis.source_version'
208 #end if
209 #if $analysis.source_uri:
210 --sourceuri '$analysis.source_uri'
211 #end if
212 #if $analysis.description:
213 --description '$analysis.description'
214 #end if
215 #if $analysis.date:
216 --date_executed '$analysis.date'
217 #end if
218
219 '$analysis.name'
220 '$analysis.program'
221 '$analysis.program_version'
222 '$analysis.source'
223 ]]></token>
224 </macros>