changeset 16:34b8e41b0a7b draft default tip

Deleted selected files

--- a/boh/birth_data.xml	Thu Sep 22 08:38:40 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<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>