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

Uploaded

<tool id="vl_import_seq_data_sample" name="VLI.seq_data_sample">
  <description>
    Import sequencing related DataSample definitions within OMERO>biobank
  </description>
  <command interpreter="bash">
    launcher.sh
    --interpreter=python
    --runner=importer.py
    #if $omero_configuration.level == 'advanced'
        --host=$omero_configuration.vl_host
        --user=$omero_configuration.vl_user
        --passwd=$omero_configuration.vl_passwd
    #else
        --host=$__user_omero_host__
        --user=$__user_omero_user__
        --passwd=$__user_omero_password__
    #end if
    --operator=$__user_email__
    --ifile=${input}
    --ofile=${output}
    --report_file=${report}
    --logfile=${logfile}
    #if $blocking_validation
      --blocking-validator
    #end if
    seq_data_sample
    #if str($study) != 'use_provided'
      --study=${study}
    #end if
    #if str($source_type) != 'use_provided'
      --source-type=${source_type}
    #end if
    #if str($seq_dsample_type) != 'use_provided'
      --seq-dsample-type=${seq_dsample_type}
    #end if
    #if str($dsample_status) != 'use_provided'
      --status=${dsample_status}
    #end if
    #if str($device) != 'use_provided'
      --device=${device}
    #end if
    #if str($history) != 'None'
      --history=${history}
    #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="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="FlowCell">FlowCell</option>
      <option value="SequencerOutput">
	SequencerOutput
      </option>
      <option value="RawSeqDataSample">
	RawSeqDataSample
      </option>

    </param>

    <!-- Choose the device after the type selection, SequencerOutput
	 will required an HardwareDevice, RawSeqDataSample and SeqDataSample
	 will required a SoftwareDevice. If the "use provided" is selected,
	 load a generic Device select list -->
    <param name="seq_dsample_type" type="select"
	   label="Type of the DataSample"
	   help="Choose from the following. See below.">
      <option value="use_provided" selected="true">
	Use record provided
      </option>
      <option value="SequencerOutput">
	SequencerOutput
      </option>
      <option value="RawSeqDataSample">
	RawSeqDataSample
      </option>
      <option value="SeqDataSample">
	SeqDataSample
      </option>
      <option value="AlignedSeqDataSample">AlignedSeqDataSample</option>
    </param>

    <param name="dsample_status" type="select" label="DataSample status" ajax = "True" ajax-source = "galaxy/get/data_sample_status" sort="True"
	   help="Choose from one of the available values. See below.">
        <option value="use_provided" selected="true">Records provide status</option>
    </param>

    <param name="device" type="select" label="device" ajax = "True" ajax-source = "galaxy/get/devices" sort="True"
	   help="Choose from the already defined devices. See below.">
         <option value="use_provided" selected="true">Records provide device ids</option>
    </param>

    <param format="txt" name="history" type="data" optional="true"
	   label="Objects history"
	   help="Galaxy history in JSON format, history will be shared among all objects"/>

    <!-- ************************************************** -->
    <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="omero_configuration">
      <param name="level" type="select" label="Configuration level">
        <option value="default" selected="true">Default: use Galaxy's preferences</option>
        <option value="advanced">Advanced: specify different host, user
        and password</option>
      </param>
      <when value="default"/>
      <when value="advanced">
        <param name="vl_host" size="40" type="text" value="hostname"
               label="OMERO.biobank host"/>
        <param name="vl_user" size="40" type="text" value="user"
               label="OMERO.biobank user"/>
        <param name="vl_passwd" size="40" type="text" value="password"
               label="OMERO.biobank 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 a tsv file with the following columns::

 study   label      source   source_type  seq_dsample_type  status  device
 FOOBAR  seq_out_1  V012141  FlowCell     SequencerOutput   USABLE  V123141
 FOOBAR  seq_out_2  V012141  FlowCell     SequencerOutput   USABLE  V123141
 FOOBAR  seq_out_3  V1AD124  FlowCell     SequencerOutput   USABLE  V123141
 ...

where
  * seq_dsample_type can assume one of the following values: SequencerOutput, RawSeqDataSample, SeqDataSample
  * source_type can assume one of the following values: FlowCell, SequencerOutput, RawSeqDataSample
 
study, source_type, seq_dsample_type, status and device columns can be
overwritten by using command line options.

A special case of the previous file is when seq_dsample_type is
SeqDataSample, in this case a mandatory sample column is required,
this column has to contain IDs of Tube objects.
The file will look like this

 study   label          source   source_type      seq_dsample_type  status  device   sample
 FOOBAR  seq_dsample_1  V041241  SequencerOutput  SeqDataSample     USABLE  VBB2351  V124AA41
 FOOBAR  seq_dsample_2  V051561  SequencerOutput  SeqDataSample     USABLE  VBB2351  V4151AAE
 FOOBAR  seq_dsample_3  V151561  SequencerOutput  SeqDataSample     USABLE  VBB2351  V15199CD
 ...

A file containing ax export of the Galaxy history that produced the
data that are going to be imported can be passed as input parameter,
history details must represented as a string serialized in JSON
format.
  </help>

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

</tool>