Mercurial > repos > gga > tripal_expression_add_biomaterial
comparison macros.xml @ 2:5e02721168e9 draft default tip
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author | gga |
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date | Wed, 14 Aug 2019 10:02:37 -0400 |
parents | 4843796fcbf6 |
children |
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1:4843796fcbf6 | 2:5e02721168e9 |
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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> |