Mercurial > repos > gga > tripal_analysis_sync

comparison macros.xml @ 0:c401f51b12cc draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:52:26 -0400
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children 8fea07ae5d94
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-1:000000000000 0:c401f51b12cc
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="2.0.4">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@">2.0.4</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="test_result">
54 <assert_stderr>
55 <has_text text="MissingSchema" />
56 </assert_stderr>
57 </xml>
58
59 <xml name="analysis">
60 <section name="analysis" title="Analysis" expanded="True">
61 <param name="name"
62 type="text"
63 label="The analysis name [mandatory]">
64 <expand macro="sanitized"/>
65 </param>
66
67 <param name="program"
68 type="text"
69 label="Program name [mandatory]"
70 help="Name of the program that was used to perform this analysis">
71 <expand macro="sanitized"/>
72 </param>
73 <param name="program_version"
74 type="text"
75 label="Program version [mandatory]"
76 help="Version of the program that was used to perform this analysis"/>
77 <param name="source"
78 type="text"
79 label="Source name [mandatory]"
80 help="Where this analysis comes from">
81 <expand macro="sanitized"/>
82 </param>
83
84 <param name="source_version"
85 argument="--sourceversion"
86 type="text"
87 optional="True"
88 label="Source version" />
89 <param name="source_uri"
90 argument="--sourceuri"
91 type="text"
92 optional="True"
93 label="Source URI"
94 help="URI where source data was retrieved" />
95 <param name="algorithm"
96 argument="--algorithm"
97 type="text"
98 label="Algorithm"
99 optional="True"
100 help="Algorithm of the program that was used to perform this analysis" />
101 <param name="description"
102 argument="--description"
103 type="text"
104 optional="True"
105 label="Analysis description">
106 <expand macro="sanitized"/>
107 </param>
108 <param name="date"
109 argument="--date_executed"
110 type="text"
111 optional="True"
112 label="Execution date"
113 help="Format: yyyy-mm-dd Default: Today">
114 <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
115 </param>
116 </section>
117 </xml>
118
119 <xml name="feature_rel">
120 <param name="rel_subject_re"
121 argument="--rel-subject-re"
122 type="text"
123 label="Regular expression to extract the unique name of the parent feature"
124 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
125 <expand macro="sanitized"/>
126 </param>
127
128 <param name="rel_subject_type"
129 argument="--rel-subject-type"
130 type="text"
131 label="Sequence type of the parent"
132 help="this should be a Sequence Ontology term" />
133 </xml>
134
135 <xml name="match_type">
136 <param name="match_type"
137 argument="--match-type"
138 type="select"
139 label="Match type for already loaded features">
140 <option value="uniquename" selected="true">Unique name</option>
141 <option value="name">Name</option>
142 </param>
143 </xml>
144
145 <xml name="matching">
146 <section name="matching" title="Feature matching" expanded="True">
147 <param name="query_type"
148 type="text"
149 label="The feature type of the blast query"
150 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
151
152 <param name="query_uniquename"
153 type="boolean"
154 checked="false"
155 truevalue="--query_uniquename"
156 falsevalue=""
157 label="Find blast query features using their Unique name"
158 help="Feature name will be used otherwise" />
159
160 <param name="query_re"
161 type="text"
162 optional="true"
163 label="Regular expression to extract the feature name from the blast query name"
164 help="leave empty if the first word in query name is sufficient">
165 <expand macro="sanitized"/>
166 </param>
167 </section>
168 </xml>
169
170 <xml name="sanitized">
171 <sanitizer>
172 <valid initial="string.printable">
173 <remove value="&apos;"/>
174 </valid>
175 <mapping initial="none">
176 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
177 <add source="(" target="\("/>
178 <add source=")" target="\)"/>
179 </mapping>
180 </sanitizer>
181 </xml>
182
183 <token name="@MATCHING@"><![CDATA[
184 #if str($matching.query_re):
185 --query_re '${matching.query_re}'
186 #end if
187
188 $matching.query_uniquename
189
190 --query_type '$matching.query_type'
191 ]]></token>
192
193 <token name="@ANALYSIS@"><![CDATA[
194 #if $analysis.algorithm:
195 --algorithm '$analysis.algorithm'
196 #end if
197 #if $analysis.source_version:
198 --sourceversion '$analysis.source_version'
199 #end if
200 #if $analysis.source_uri:
201 --sourceuri '$analysis.source_uri'
202 #end if
203 #if $analysis.description:
204 --description '$analysis.description'
205 #end if
206 #if $analysis.date:
207 --date_executed '$analysis.date'
208 #end if
209
210 '$analysis.name'
211 '$analysis.program'
212 '$analysis.program_version'
213 '$analysis.source'
214 ]]></token>
215 </macros>