Mercurial > repos > rnateam > data_manager_sortmerna_database_downloader

changeset 1:30bb49887172 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 044a991b45c9135339daf138929887cd8e93a1bf
author rnateam
date Tue, 06 Jun 2017 13:40:27 -0400
parents 765f4ec851f0
children 7d2252852f96
files data_manager/data_manager_sortmerna_download.py data_manager/data_manager_sortmerna_download.xml data_manager_conf.xml tool-data/rRNA_databases.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_sortmerna_download.py	Wed May 31 14:53:00 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.py	Tue Jun 06 13:40:27 2017 -0400
@@ -140,7 +140,6 @@
             data_tables,
             "rRNA_databases",
             dict(
-                dbkey=db_name,
                 value=version,
                 name=db_name,
                 path=output_filepath))
--- a/data_manager/data_manager_sortmerna_download.xml	Wed May 31 14:53:00 2017 -0400
+++ b/data_manager/data_manager_sortmerna_download.xml	Tue Jun 06 13:40:27 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.0" tool_type="manage_data">
+<tool id="data_manager_sortmerna_download" name="Download SortMeRNA" version="@VERSION@.1" tool_type="manage_data">
     <description>reference databases</description>
     <macros>
         <import>macros.xml</import>
--- a/data_manager_conf.xml	Wed May 31 14:53:00 2017 -0400
+++ b/data_manager_conf.xml	Tue Jun 06 13:40:27 2017 -0400
@@ -5,13 +5,12 @@
             <output> <!-- Handle the output of the Data Manager Tool -->
                 <column name="value" />  <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
-                <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool -->
                 <column name="path" output_ref="out_file" >
                     <move type="file">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${dbkey}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rRNA_databases/${name}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${dbkey}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rRNA_databases/${name}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/tool-data/rRNA_databases.loc.sample	Wed May 31 14:53:00 2017 -0400
+++ b/tool-data/rRNA_databases.loc.sample	Tue Jun 06 13:40:27 2017 -0400
@@ -1,2 +1,2 @@
-#<unique_id>  <database_caption>  <name>  <fasta_file_path>
+#<unique_id>  <database_caption>  <fasta_file_path>
 
--- a/tool_data_table_conf.xml.sample	Wed May 31 14:53:00 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Jun 06 13:40:27 2017 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="rRNA_databases" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
+        <columns>value, name, path</columns>
         <file path="tool-data/rRNA_databases.loc" />
     </table>
 </tables>
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