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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/importer/sequencing_data_sample.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,184 @@
+<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>