changeset 2:1e59902651e7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/birth_data.xml	Fri Sep 16 08:56:27 2016 -0400
@@ -0,0 +1,82 @@
+<tool id="vl_import_birth_data" name="VLI.birth_data">
+  <description>import diagnosis data within omero/vl</description>
+  <command interpreter="python">
+    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
+    #else #unauthorized_access.py
+    #end if
+    #if $advanced_configuration.configuration_level == 'advanced'
+      --host=$advanced_configuration.vl_host
+      --user=$advanced_configuration.vl_user
+      --passwd=$advanced_configuration.vl_passwd
+    #end if
+    --operator=galaxy
+    --ifile=$input
+    --report_file=$report
+    --loglevel=$__app__.config.vl_loglevel
+    --logfile=${logfile}
+    birth_data
+    #if str($study) != 'use_provided'
+      --study ${study}
+    #end if 
+  </command>  
+
+  <inputs>
+    <param format="tabular" name="input" type="data"
+	   label="A tabular dataset with the following columns ..."/>
+
+    <param name="study" type="select" label="Context study" 
+	   help="Choose from the already defined studies. See below.">    
+      <options from_parameter="tool.app.known_studies" 
+	       transform_lines="[ &quot;%s%s%s:%s&quot; 
+                                  % ( l[0], self.separator, l[0], l[1][:40] ) 
+                                  for l in obj ]">
+        <column name="value" index="0"/>
+        <column name="name" index="1"/>
+        <filter type="sort_by" column="0"/>
+        <filter type="add_value" name="Records provide study labels" 
+                value="use_provided" index="0"/>
+      </options>
+    </param>
+
+    <!-- ************************************************** -->
+    <conditional name="advanced_configuration">
+      <param name="configuration_level" type="select" 
+	     label="Configuration level">
+	<option value="default" selected="true">Default configuration</option>	
+	<option value="advanced">Advanced configuration</option>
+      </param>
+      <when value="default"/>
+      <when value="advanced">
+	<param name="vl_host" size="40" type="text" value="localhost" 
+	       label="Omero/VL host"/>
+	<param name="vl_user" size="20" type="text" value="root" 
+	       label="Omero/VL user"/>
+	<param name="vl_passwd" size="20" type="text" value="What?Me worry?" 
+	       label="Omero/VL passwd"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="report" label="${tool.name}.report"/>
+    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
+  </outputs>
+
+  <help>
+Will read in a tsv file with the following columns::
+
+  study   individual   timestamp      birth_date   birth_place
+  ASTUDY  V1234        1310057541608  12/03/1978   006171
+  ASTUDY  V14112       1310057541608  25/04/1983   006149
+  ASTUDY  V1241        1310057541608  12/03/2001   006172
+  .....
+
+where birth_place is a valid ISTAT code for an Italian city or a
+foreign Country and birth_date must have the dd/mm/YYYY format.
+  </help>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+</tool>