view biosample.xml @ 12:46f08bb8dd68 draft default tip

Uploaded

<tool id="vl_import_biosample" name="VLI.biosample">
  <description>import BioSample 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 $blocking_validation
      --blocking-validator
    #end if
    biosample
    #if str($study) != 'use_provided'
      --study ${study}
    #end if
    #if str($source_type) != 'use_provided'
      --source-type ${source_type}
    #end if
    #if str($vessel_type_selector.vessel_type) != 'use_provided'
      --vessel-type ${vessel_type_selector.vessel_type}
    #end if
    #if str($vessel_content) != 'use_provided'
      --vessel-content=${vessel_content}
    #end if
    #if str($vessel_status) != 'use_provided'
      --vessel-status=${vessel_status}
    #end if
    #if str($vessel_type_selector) == 'IlluminaBeadChipArray'
        #if str($vessel_type_selector.assay_type) != 'use_provided'
            --bead-chip-assay-type=${vessel_type_selector.assay_type}
        #end if
    #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 object"
	   help="Choose from the legal types. See below.">
      <option value="use_provided" selected="true">
      Use what provided by record</option>
      <option value="Tube">Tube</option>
      <option value="PlateWell">PlateWell</option>
      <option value="Individual">Individual</option>
      <option value="NO_SOURCE">No source provided</option>
    </param>

    <conditional name="vessel_type_selector">
        <param name="vessel_type" type="select"
	      label="type of the vessel object"
	      help="Choose from the legal types. See below.">
            <option value="use_provided" selected="true">
                Use what provided by record
            </option>
            <option value="Tube">Tube</option>
            <option value="PlateWell">PlateWell</option>
            <option value="IlluminaBeadChipArray">IlluminaBeadChipArray</option>
        </param>
        <when value="IlluminaBeadChipArray">
            <param name="assay_type" type="select" label="Illumina Bead Chip Array Assay type"
                   help="Choose from the following assay types">
                <options from_parameter="tool.app.known_illumina_beadchip_assay_type"
                         transform_lines="[ &quot;%s%s%s&quot;
                                          % (o[1], self.separator, o[1])
                                          for o 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 assay type"
                            value="use_provided" index="0"/>
                </options>
            </param>
        </when>
    </conditional>

    <param name="vessel_content" type="select" label="Vessel content" 
	   help="Choose from one of the available values. See below.">    
      <options from_parameter="tool.app.kb.VesselContent.__enums__" 
	       transform_lines="[ &quot;%s%s%s&quot; 
                                  % (e.enum_label(),
                                     self.separator,
                                     e.enum_label()) 
                                  for e 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 vessel content" 
                value="use_provided" index="0"/>
      </options>
    </param>
    <param name="vessel_status" type="select" label="Vessel status" 
	   help="Choose from one of the available values. See below.">    
      <options from_parameter="tool.app.kb.VesselStatus.__enums__" 
	       transform_lines="[ &quot;%s%s%s&quot; 
                                  % (e.enum_label(),
                                     self.separator,
                                     e.enum_label()) 
                                  for e 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 vessel status" 
                value="use_provided" index="0"/>
      </options>
    </param>

    <conditional name="extra_fields">
      <param name="enabled" type="select" 
	     label="Enable extra optional fields">
	<option value="no" selected="true">no</option>	
	<option value="yes">yes</option>
      </param>
      <when value="no"/>
      <when value="yes">
	<param name="current_volume" type="float"
	       value="20" 
	       help="fluid (FIXME UNITS) currently held in the vessel">
	  <validator type="in_range" message="Volume must be positive" 
		     min="0" max="inf"/>
	</param>
	<param name="used_volume" type="float"
	       value="20" 
	       help="amount of source fluid (FIXME UNITS) used">
	  <validator type="in_range" message="Volume must be positive" 
		     min="0" max="inf"/>
	</param>
      </when>
    </conditional>

    <!-- ************************************************** -->
    <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>
A biosample record will have, at least, the following fields::

  label     source
  I001-bs-2 V932814892
  I002-bs-2 V932814892
  I003-bs-2 None

Where label is the label of the biosample container. If a 'None' value
has been passed in the source column, the biosample will be imported
as a new unlinked object into the biobanks. Another example, this time
involving DNA samples::

  label    source     used_volume current_volume activation_date
  I001-dna V932814899 0.3         0.2            17/03/2007
  I002-dna V932814900 0.22        0.2            21/01/2004

A special case is when records refer to biosamples contained in plate
wells. In this case, an additional column must be present with the VID
of the corresponding TiterPlate object. For instance::

  plate  label source
  V39030 A01   V932814892
  V39031 A02   V932814893
  V39032 A03   V932814894

where the label column is now the label of the well position.

If row and column (optional) are provided, the program will use them;
if they are not provided, it will infer them from label (e.g., J01 ->
row=10, column=1). Missing labels will be generated as::

  '%s%03d' % (chr(row+ord('A')-1), column)

A badly formed label will result in the rejection of the record; the
same will happen if label, row and column are inconsistent. The well
will be filled by current_volume material produced by removing
used_volume material taken from the bio material contained in the
vessel identified by source. row and column are base 1.

If the sample is a IlluminaBeadChipArray the plate column used in the
PlateWell case will become a illumina_array column and a new column, named
bead_chip_assay_type, is required::

  illumina_array  label   source   bead_chip_assay_type
  V1351235        R01C01  V412441  HUMANEXOME_12V1_B
  V1351235        R01C02  V351151  HUMANEXOME_12V1_B
  V1351235        R02C01  V345115  HUMANEXOME_12V1_B
  </help>

  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>

</tool>