Mercurial > repos > gga > tripal_organism_sync

comparison macros.xml @ 6:afd5d92745fb draft default tip

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author gga
date Wed, 14 Aug 2019 10:06:05 -0400
parents 9f1f23daff7b
children
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5:9f1f23daff7b 6:afd5d92745fb
39 ]]></token> 39 ]]></token>
40 40
41 <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token> 41 <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
42 42
43 <token name="@AUTH@"><![CDATA[ 43 <token name="@AUTH@"><![CDATA[
44 echo "__default: local" > '.auth.yml' && 44 if [ -z "\$TRIPAILLE_GLOBAL_CONFIG_PATH" ]; then
45 echo "local:" >> '.auth.yml' && 45 echo "__default: local" > '.auth.yml' &&
46 echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' && 46 echo "local:" >> '.auth.yml' &&
47 echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' && 47 echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
48 echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' && 48 echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
49 49 echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
50 TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml' 50
51 export TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
52 ; fi &&
51 ]]></token> 53 ]]></token>
52 54
53 <xml name="wait_for"> 55 <xml name="wait_for">
54 <param name="wait_for" 56 <param name="wait_for"
55 type="data" 57 type="data"
153 155
154 <xml name="matching"> 156 <xml name="matching">
155 <section name="matching" title="Feature matching" expanded="True"> 157 <section name="matching" title="Feature matching" expanded="True">
156 <param name="query_type" 158 <param name="query_type"
157 type="text" 159 type="text"
158 label="The feature type of the blast query" 160 label="The feature type of the query"
159 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" /> 161 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
160 162
161 <param name="query_uniquename" 163 <param name="query_uniquename"
162 type="boolean" 164 type="boolean"
163 checked="false" 165 checked="false"
164 truevalue="--query_uniquename" 166 truevalue="--query_uniquename"
165 falsevalue="" 167 falsevalue=""
166 label="Find blast query features using their Unique name" 168 label="Find query features using their Unique name"
167 help="Feature name will be used otherwise" /> 169 help="Feature name will be used otherwise" />
168 170
169 <param name="query_re" 171 <param name="query_re"
170 type="text" 172 type="text"
171 optional="true" 173 optional="true"
172 label="Regular expression to extract the feature name from the blast query name" 174 label="Regular expression to extract the feature name from the query name"
173 help="leave empty if the first word in query name is sufficient"> 175 help="leave empty if the first word in query name is sufficient">
174 <expand macro="sanitized"/> 176 <expand macro="sanitized"/>
175 </param> 177 </param>
176 </section> 178 </section>
177 </xml> 179 </xml>