# HG changeset patch
# User ric
# Date 1474547884 14400
# Node ID b764aabef6f0449e6760e6be5e00c681e4c336ea
# Parent  5ceb7668e2591216aca25a418bfd439102db2ef7
Deleted selected files

diff -r 5ceb7668e259 -r b764aabef6f0 boh/data_object.xml
--- a/boh/data_object.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-<tool id="vl_import_data_object" name="VLI.data_object">
-  <description>import DataObject 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 $blocking_validation
-      --blocking-validator
-    #end if
-    data_object
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    #if str($mimetype) != 'use_provided'
-      --mimetype=${mimetype}
-    #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="mimetype" type="select"
-	   label="mimetype for the data object."
-	   help="Choose from the following. See below.">
-      <option value="use_provided"       selected="true">
-      Use record provided</option>
-      <option value="x-vl/affymetrix-cel">x-vl/affymetrix-cel</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 path data_sample mimetype size sha1
-
-   TEST01 file:/share/fs/v039303.cel V2902 x-vl/affymetrix-cel 39090 E909090
-  ....
-
-Records that point to an unknown data sample will be noisily
-ignored. The same will happen to records that have the same path of a
-previously seen data_object
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 5ceb7668e259 -r b764aabef6f0 boh/data_sample.xml
--- a/boh/data_sample.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-<tool id="vl_import_data_sample" name="VLI.data_sample">
-  <description>import DataSample 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 $blocking_validation
-      --blocking-validator
-    #end if
-    data_sample
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    #if str($source_type) != 'use_provided'
-      --source-type=${source_type}
-    #end if
-    #if str($device_type) != 'use_provided'
-      --device-type=${device_type}
-    #end if
-    #if str($scanner) != 'use_provided'
-      --scanner=${scanner}
-    #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="source_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="Individual">Individual</option>
-      <option value="Tube">Tube</option>
-      <option value="PlateWell">PlateWell</option>
-      <option value="DataSample">DataSample</option>
-      <option value="DataCollectionItem">DataCollectionItem</option>
-      <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
-      <option value="IlluminaBeadChipMeasures">IlluminaBeadChipMeasures</option>
-    </param>
-
-    <param name="device_type" type="select"
-	   label="Type of the device"
-	   help="Choose from the following. See below.">
-      <option value="use_provided"       selected="true">
-      Use record provided</option>
-      <option value="Device">Device</option>
-      <option value="Chip">Chip</option>
-      <option value="SoftwareProgram">SoftwareProgram</option>
-    </param>
-
-    <param name="scanner" type="select" label="Scanner used" 
-	   help="Choose from the possible scanners. See below.">    
-      <options from_parameter="tool.app.known_scanners" 
-	       transform_lines="[ &quot;%s%s%s(%s)&quot; 
-                                  % ( l[0], self.separator, l[1], l[2]) 
-                                  for l in obj ]">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <filter type="sort_by" column="1"/>
-        <filter type="add_value" name="Records provide scanner ids" 
-                value="use_provided" index="0"/>
-      </options>
-    </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 source device device_type scanner options
-  ASTUDY foo01 v03909 v9309  Chip        v99020  celID=0009099090
-  ASTUDY foo02 v03909 v99022 Scanner     v99022  conf1=...,conf2=...
-  ....
-
-In this example, the first line corresponds to a dataset obtained by
-using chip v9309 on scanner v99020, while the second datasample has
-been obtained using a technology directly using a scanner, e.g., an
-Illumina HiSeq 2000. The '''scanner''' column is there as a
-convenience to support a more detailed description of a chip-based
-acquisition.
-
-The general strategy is to decide what data objects should be
-instantiated by looking at the chip column and at its corresponding
-maker,model,release.
-
-The optional column '''scanner''', the vid of the scanner device, is
-used in cases, such as Affymetrix genotyping, where it is relevant.
-
-It is also possible to import DataSample(s) that are the results of
-processing other DataSample(s). Here is an example::
-
-  study  label source device device_type     options
-  ASTUDY foo01 v03909 v99021 SoftwareProgram conf1=...,conf2=...
-  ASTUDY foo02 v03909 v99021 SoftwareProgram conf1=...,conf2=...
-  ....
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 5ceb7668e259 -r b764aabef6f0 boh/device.xml
--- a/boh/device.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-<tool id="vl_import_device" name="VLI.device">
-  <description>import Device 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 $blocking_validation
-      --blocking-validator
-    #end if
-    device
-    #if str($study) != 'use_provided'
-      --study ${study}
-    #end if 
-    #if str($device_type) != 'use_provided'
-      --device-type=${device_type}
-    #end if
-    #if str($maker)
-      --maker=${maker}
-    #end if
-    #if str($model)
-      --model=${model}
-    #end if
-    #if str($release)
-      --relese=${release}
-    #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="device_type" type="select"
-	   label="type of the device"
-	   help="Choose from the following. See below.">
-      <option value="use_provided"       selected="true">
-      Use record provided</option>
-      <option value="Chip">Chip</option>
-      <option value="Scanner">Scanner</option>
-      <option value="SoftwareProgram">SoftwareProgram</option>
-      <option value="GenotypingProgram">GenotypingProgram</option>
-    </param>
-
-    <param name="maker" size="40" type="text" value=""  label="Device maker"/>
-    <param name="model" size="40" type="text" value=""  label="Device model"/>
-    <param name="release" size="40" type="text" value="" 
-	   label="Device release"/>
-
-    <!-- ************************************************** -->
-    <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  device_type    label   barcode maker model release location
-  BSTUDY Scanner pula01  8989898 Affymetrix  GeneChip Scanner 3000 7G  Pula bld. 5
-  BSTUDY Chip    chip001 8329482 Affymetrix  Genome-Wide Human SNP Array 6.0  None
-
-All devices have a type, a label, an optional barcode, a maker, a
-model, a release and an optional physical location. In the example
-above, in the first line we have defined a scanner, which is
-physically located in the building 5 lab in Pula.  The second line
-defines a chip.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 5ceb7668e259 -r b764aabef6f0 boh/diagnosis.xml
--- a/boh/diagnosis.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-<tool id="vl_import_diagnosis" name="VLI.diagnosis">
-  <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}
-    diagnosis
-    #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      diagnosis
-   ASTUDY V899       1310057541608  icd10-cm:E10
-   ASTUDY V899       1310057541608  icd10-cm:G35
-   ASTYDY V1806      1310057541608  exclusion-problem_diagnosis
-   ...
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 5ceb7668e259 -r b764aabef6f0 boh/enrollment.xml
--- a/boh/enrollment.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-<tool id="vl_import_enrollment" name="VLI.enrollment">
-  <description>Create new enrollmnents for existing individuals 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 str($advanced_configuration.configuration_level) == 'advanced'
-      --host=$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 $blocking_validation
-      --blocking-validator
-    #end if
-    enrollment
-    #if str($study_label) != 'use_provided'
-      --study=$study_label
-    #end if
-  </command>
-
-  <inputs>
-    <param format="tabular" name="input" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-
-    <param name="study_label" type="select" label="Context study"
-	   help="Choose from 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 will provide study labels"
-		value="use_provided" index="0"/>
-      </options>
-    </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>
-Import of new enrollments related to existing individuals.
-An enrollment is characterized by the following fields::
-
- source                              study  label
- V044DE795E7F9F42FEB9855288CF577A77  xxx    id1
- V06C59B915C0FD47DABE6AE02C731780AF  xxx    id2
- V01654DCFC5BB640C0BB7EE088194E629D  xxx    id3
-
-where source must be the VID of an existing Individual object, study a
-label of an existing Study object and label the enrollment code for
-the patient in the study.
-
-The enrollment sub-operation will retrieve the source individual from
-the DB, create a new enrollment related to it and output the VIDs of
-newly created enrollments. It is not possible to create two
-enrollments with the same code related to the same study, nor is it
-possible to enroll a patient twice in the same study, even with
-different codes.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
\ No newline at end of file
diff -r 5ceb7668e259 -r b764aabef6f0 boh/group.xml
--- a/boh/group.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-<tool id="vl_import_group" name="VLI.group">
-  <description>Create a new group 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 str($advanced_configuration.configuration_level) == 'advanced'
-      --host=$advanced_configuration.vl_host
-      --user=$advanced_configuration.vl_user
-      --passwd=$advanced_configuration.vl_passwd
-    #end if
-    --operator=galaxy
-    --ifile=$input1
-    --ofile=$output1
-    --loglevel=$__app__.config.vl_loglevel
-    --logfile=${logfile}
-    group
-   #if str($group_label) != ''
-    --group=$group_label
-   #end if
-  </command>  
-
-  <inputs>
-    <param format="tabular" name="input1" type="data"
-	   label="A tabular dataset with the following columns ..."/>
-
-    <param name="group_label" size="40" type="text" 
-	   value="" 
-	   label="New group label"/>
-
-    <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="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>
-      <when/>
-    </conditional>
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="output1" label="${tool.name}.mapping"/>
-    <data format="txt" name="logfile"     label="${tool.name}.logfile"/>
-  </outputs>
-
-  <help>
-Will create a new group of individuals from a file with the following columns::
-
-   study   label   individual
-   foo     I0000   V06C59B915C0FD47DABE6AE02C731780AF
-   foo     I0001   V0B718B77691B145BFA8901FCCF6B37998
-   ...
-
-where the column study is optional (it can be provided via the
-group_label param). Labels should be unique within the file and the
-individual field should contain VIDs of existing (within omero/vl)
-Individual objects.
-  </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>
diff -r 5ceb7668e259 -r b764aabef6f0 boh/illumina_bead_chip_measures.xml
--- a/boh/illumina_bead_chip_measures.xml	Thu Sep 22 08:37:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +0,0 @@
-<tool id="vl_import_illumina_bead_chip_measures" name="VLI.illumina_bead_chip_measures">
-    <description>import IlluminaBeadChipMeasures definitions within OMERO</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 $blocking_validation
-            --blocking-validator
-        #end if
-        illumina_bead_chip_measures
-        #if str($study) != 'use_provided'
-            --study=${study}
-        #end if
-        #if str($source_type) != 'use_provided'
-            --source_type=${source_type}
-        #end if
-        #if str($action_category) != 'use_provided'
-            --action_category=${action_category}
-        #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="source_type" type="select"
-               label="Type of the source"
-               help="Choose from the following source classes. See below.">
-            <option value="use_provided" selected="true">Use record provided</option>
-            <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
-        </param>
-
-        <param name="action_category" type="select"
-               label="Action category"
-               help="Choose from the following action categories. See below.">
-            <options from_parameter="tool.app.known_action_categories"
-                     transform_lines="[ &quot;%s%s%s&quot;
-                                        % ( l[1], self.separator, l[1] )
-                                        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 action category"
-                        value="use_provided" index="0"/>
-            </options>
-        </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="biobank05.crs4.it"
-                       label="OMERO host"/>
-                <param name="vl_user" size="40" type="text" value="galaxy"
-                       label="OMERO user"/>
-                <param name="vl_passwd" size="40" type="text" value="What? Me worry?"
-                       label="OMERO password"/>
-            </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 a tsv file with the following columns::
-
-  study   label           red_channel     green_channel     source         source_type
-  ASTUDY  CHIP_01_R01C01  V1415151235513  V135135661356161  V351351351551  IlluminaBeadChipArray
-  ASTUDY  CHIP_01_R01C02  V2346262462462  V112395151351623  V135113513223  IlluminaBeadChipArray
-  ASTUDY CHIP_01_R02C01   V1351362899135  V913977551235981  V100941215192  IlluminaBeadChipArray
-
-This will create new IlluminaBeadChipMeasures whose labels are defined in the
-label column.
-    </help>
-
-  <stdio>
-    <exit_code range="1:" level="fatal" />
-  </stdio>
-
-</tool>