diff galaxy-tools/biobank/importer/data_sample.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/importer/data_sample.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,165 @@
+<tool id="vl_import_data_sample" name="VLI.data_sample">
+  <description>import 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 $blocking_validation
+      --blocking-validator
+    #end if
+    data_sample
+    #if str($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=${scanner}
+    #end if
+    #if str($data_sample_type) != 'use_provided'
+      --data-sample-type=${data_sample_type}
+    #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="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="data_sample_type" type="select"
+	   label="Type of the data sample"
+	   help="Choose from the following. See below.">
+      <option value="use_provided"       selected="true">
+      Use record provided</option>
+      <option value="GenotypeDataSample">GenotypeDataSample</option>
+      <option value="IlluminaBeadChipMeasure">IlluminaBeadChipMeasure</option>
+      <option value="GenomeVariationsDataSample">GenomeVariationsDataSample</option>
+    </param>
+
+    <param name="scanner" type="select" label="Scanner used" ajax = "True" ajax-source = "galaxy/get/scanners" sort="True"
+	   help="Choose from the possible scanners. See below.">    
+     <option value="use_provided" selected="true">Records provide scanner ids</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="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>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <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>
+</tool>