Mercurial > repos > dchristiany > frogs_data_manager

changeset 6:d11bc4a8f596 draft

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planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty
author dchristiany
date Thu, 03 Oct 2019 10:29:39 -0400
parents ac4fb9d97a51
children 99b2dfb1fa1c
files data_manager/FROGS_data_manager.py data_manager/FROGS_data_manager.xml data_manager_conf.xml
diffstat 3 files changed, 8 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/FROGS_data_manager.py	Thu Oct 03 05:10:33 2019 -0400
+++ b/data_manager/FROGS_data_manager.py	Thu Oct 03 10:29:39 2019 -0400
@@ -83,5 +83,9 @@
     elif args.database=="phiX_db_data":
         phiX_sources(args.resource)
 
+    #save info to json file
+    filename = args.output
+    open(filename, 'wb').write(to_json_string(data_manager_dict))
+
 if __name__ == "__main__":
     main()
--- a/data_manager/FROGS_data_manager.xml	Thu Oct 03 05:10:33 2019 -0400
+++ b/data_manager/FROGS_data_manager.xml	Thu Oct 03 10:29:39 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.03" tool_type="manage_data">
+<tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.03.1" tool_type="manage_data">
     <requirements>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
-    <command detect_errors="exit_code"><![CDATA[
+    <command><![CDATA[
         python $__tool_directory__/FROGS_data_manager.py
             --database="$database.database"
             --output "$output"
@@ -18,14 +18,8 @@
             </param>
             <when value="frogs_db_data"/>
             <when value="HVL_db_data">
-                <param name="resource" type="select" label="Choose the resource to create/update">
-                    <option value="unite_7.1_ITS1">UNITE 7.1 ITS1</option>
-                </param>
             </when>
             <when value="phiX_db_data">
-                <param name="resource" type="select" label="Choose the resource to create/update">
-                    <option value="phiX">phiX</option>
-                </param>
             </when>
         </conditional>
     </inputs>
--- a/data_manager_conf.xml	Thu Oct 03 05:10:33 2019 -0400
+++ b/data_manager_conf.xml	Thu Oct 03 10:29:39 2019 -0400
@@ -7,10 +7,10 @@
                 <column name="name" />
                 <column name="path" output_ref="output" >
                     <move type="directory">
-                        <source>#echo "/".join(str(${path}).split('/')[:-1])#</source>
+                        <source>#echo "/".join(str($path).split('/')[:-1])#</source>
                         <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">frogs_db</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/frogs_db/#echo "/".join(str(${path}).split('/')[-2:])#</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/frogs_db/#echo "/".join(str($path).split('/')[-2:])#</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>