diff gdcwebapp.xml @ 10:c0be9583df97 draft

Uploaded 20170525

--- a/gdcwebapp.xml	Thu May 25 15:49:07 2017 -0400
+++ b/gdcwebapp.xml	Thu May 25 17:58:15 2017 -0400
@@ -1,25 +1,24 @@
 <?xml version="1.0"?>
 <tool name="GDCWebApp" id="data_source_gdcwebapp" tool_type="data_source" hidden="False" display_interface="False" version="1.0.0" force_history_refresh="True">
     <description>an intuitive interface to filter, extract, and convert Genomic Data Commons experiments</description>
-    <requirements>
-        <requirement type="package" version="2.7.10">python</requirement>
-        <!--<requirement type="package" version="1.0.0">galaxy_json_data_source</requirement>-->
-    </requirements>
     <stdio>
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-    <!--<version_command>json_data_source.py --version</version_command>-->
-    <!--<command>json_data_source.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "."</command>-->
-    <command interpreter="python">json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}"</command>
+    <command>
+        <![CDATA[
+            mkdir -p ${tool.name}_tmp && 
+            python ${__tool_directory__}/json_data_source_mod.py "${__app__.config.output_size_limit}" --json_param_file "${output1}" --path "." --appdata "${tool.name}_tmp"
+        ]]>
+    </command>
     <inputs check_values="False" action="http://bioinf.iasi.cnr.it/gdcwebapp/app.php" >
         <display>Go to GDCWebApp service $GALAXY_URL</display>
         <param name="URL" type="hidden" value="" />
     </inputs>
     <outputs>
-        <data name="output1" format="auto" />
-        <collection name="list_output" type="list:list" label="${tool.name} output">
-            <discover_datasets pattern="(?P&lt;archive_name&gt;.*)_(?P&lt;file_name&gt;.*)\..*" ext="auto" visible="True" directory="${tool.name}" />
+        <data name="output1" format="auto" visible="False" />
+        <collection name="list_output" type="list:list" label="${tool.name} Output Collection">
+            <discover_datasets pattern="(?P&lt;archive_name&gt;.*)_(?P&lt;file_name&gt;.*)\..*" ext="auto" visible="True" directory="${tool.name}_tmp" />
         </collection>
     </outputs>
     <options sanitize="False" refresh="True" />