view galaxy-tools/biobank/importer/data_object.xml @ 0:ba6cf6ede027 draft default tip

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<tool id="vl_import_data_object" name="VLI.data_object">
  <description>import DataObject definitions within omero/vl</description>
  <command interpreter="bash">
    launcher.sh
    --interpreter=python
    --runner=importer.py
    --host=$__user_omero_host__
    --user=$__user_omero_user__
    --passwd=$__user_omero_password__
    --operator=$__user_email__
    --ifile=${input}
    --ofile=${output}
    --report_file=${report}
    --logfile=${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" ajax = "True" ajax-source = "galaxy/get/studies" sort="True"
           help="Choose from the already defined studies. See below.">
		<option value="use_provided" selected="true">Records provide study labels</option>
    </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>

  </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>

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

  <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>
</tool>