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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/importer/data_object.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,82 @@
+<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>