changeset 15:9fc9fc2a958f draft

Deleted selected files

--- a/boh/data_collection.xml	Thu Sep 22 08:38:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-<tool id="vl_import_data_collection" name="VLI.data_collection">
-  <description>import DataCollection definitions 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=$input
-    --ofile=$output
-    --report_file=$report
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    #if $blocking_validation
-      --blocking-validator
-    #end if
-    data_collection
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    #if str($data_sample_type) != 'use_provided'
-      --data_sample-type=${data_sample_type}
-    #end if
-    #if str($label)
-      --label=${label}
-    #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>
-
-    <param name="label" size="20" type="text" value="" 
-	   label="collection label"/>
-
-    <param name="data_sample_type" type="select"
-	   label="Type of the source"
-	   help="Choose from the following. See below.">
-      <option value="use_provided"       selected="true">
-      Use record provided</option>
-      <option value="DataSample">DataSample</option>
-    </param>
-
-
-    <!-- ************************************************** -->
-    <param name="blocking_validation" type="boolean" checked="false"
-	   label="Blocking validation"
-	   help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
-
-    <conditional name="wait_for_trigger">
-      <param name="enable_trigger" type="boolean" checked="false"
-	     label="Wait for another tool to end before running this tool"/>
-      <when value="true">
-	<param format="txt" name="trigger_file" type="data"
-	       label="Select the LOG file that will be used as trigger"/>
-      </when>
-    </conditional>
-
-    <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="output" label="${tool.name}.mapping"/>
-    <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    label data_sample
-  BSTUDY   dc-01 V0390290
-  BSTUDY   dc-01 V0390291
-  BSTUDY   dc-02 V0390292
-  BSTUDY   dc-02 V390293
-  ...
-
-This will create new DataCollection(s), whose label is defined by the
-label column, and link to it, using DataCollectionItem objects,
-the DataSample object(s) identified by data_sample (a VID).
-
-Records that point to an unknown DataSample will abort the data
-collection loading. Previously seen collections will be noisily
-ignored. It is not legal to use the importer to add items to a
-previously known collection.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>