Mercurial > repos > gga > tripal_expression_add_biomaterial

changeset 2:5e02721168e9 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 10:02:37 -0400
parents 4843796fcbf6
children
files expression_add_biomaterial.xml macros.xml
diffstat 2 files changed, 14 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/expression_add_biomaterial.xml	Tue Mar 05 05:24:55 2019 -0500
+++ b/expression_add_biomaterial.xml	Wed Aug 14 10:02:37 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.0">
+<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.1">
  <description>in Tripal</description>
     <macros>
         <import>macros.xml</import>
@@ -30,6 +30,8 @@
         <!-- arguments -->
         <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
         <param name="file_path" label="Biomaterial description sheet" argument="file_path" type="data" format="xml,tsv,csv" help="A file describing the biomaterial" />
+
+        <expand macro="wait_for"/>
     </inputs>
     <outputs>
         <data format="txt" name="results"/>
--- a/macros.xml	Tue Mar 05 05:24:55 2019 -0500
+++ b/macros.xml	Wed Aug 14 10:02:37 2019 -0400
@@ -41,13 +41,15 @@
     <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
 
     <token name="@AUTH@"><![CDATA[
-        echo "__default: local" > '.auth.yml' &&
-        echo "local:" >> '.auth.yml' &&
-        echo "    tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
-        echo "    username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
-        echo "    password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
+        if [ -z "\$TRIPAILLE_GLOBAL_CONFIG_PATH" ]; then
+          echo "__default: local" > '.auth.yml' &&
+          echo "local:" >> '.auth.yml' &&
+          echo "    tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
+          echo "    username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
+          echo "    password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
 
-        TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
+          export TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
+        ; fi &&
     ]]></token>
 
     <xml name="wait_for">
@@ -155,7 +157,7 @@
         <section name="matching" title="Feature matching" expanded="True">
             <param name="query_type"
                    type="text"
-                   label="The feature type of the blast query"
+                   label="The feature type of the query"
                    help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
 
             <param name="query_uniquename"
@@ -163,13 +165,13 @@
                    checked="false"
                    truevalue="--query_uniquename"
                    falsevalue=""
-                   label="Find blast query features using their Unique name"
+                   label="Find query features using their Unique name"
                    help="Feature name will be used otherwise" />
 
             <param name="query_re"
                    type="text"
                    optional="true"
-                   label="Regular expression to extract the feature name from the blast query name"
+                   label="Regular expression to extract the feature name from the query name"
                    help="leave empty if the first word in query name is sufficient">
                 <expand macro="sanitized"/>
             </param>