diff galaxy-tools/biobank/utils/prepare_seq_dsample_inputs.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/prepare_seq_dsample_inputs.xml	Wed Sep 28 06:03:30 2016 -0400
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+<tool id="vl_prepare_seq_dsample_inputs" 
+      name="VLUTIL.prepare_seq_dsample_inputs">
+  <description>
+    Extract OMERO.biobank objects from a sequencing samplesheet
+  </description>
+
+  <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=prepare_seq_dsample_inputs.py
+    --in-file=${infile}
+    --logfile=${log_file}
+    --tubes-out-file=${tubes_ofile}
+    --flowcells-out-file=${flowcells_ofile}
+    --lanes-out-file=${lanes_ofile}
+    --laneslots-out-file=${laneslots_ofile}
+    --config-parameters=${config_params}
+    --study-output-file=${study_ofile}
+    --tubes-subsamples-output-file=${subsamples_ofile}
+  </command>
+
+  <inputs>
+    <param format="tabular" name="infile" type="data"
+	   label="Sampelsheet (in TAB-separated format)"/>
+    <param format="txt" name="config_params" type="data"
+	   label="Configuration parameters" optional="false"/>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="tubes_ofile"
+	  label="${tool.name}_tubes.tsv"/>
+    <data format="tabular" name="subsamples_ofile"
+	  label="${tool.name}_subsamples.tsv"/>
+    <data format="tabular" name="flowcells_ofile"
+	  label="${tool.name}_flowcells.tsv"/>
+    <data format="tabular" name="lanes_ofile"
+	  label="${tool.name}_lanes.tsv"/>
+    <data format="tabular" name="laneslots_ofile"
+	  label="${tool.name}_laneslots.tsv"/>
+    <data format="tabular" name="study_ofile"
+	  label="${tool.name}_study.tsv"/>
+    <data format="txt" name="log_file"
+	  label="${tool.name}.log"/>
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+This tool produces files that can be used as input to import
+ * samples
+ * flowcells
+ * lanes
+ * laneslots
+
+within OMERO.biobank using import applications.
+
+If the optional 'study-output-file' parameter is given as input, the
+script will produce the input file for a new study definition.
+
+If the optional 'tubes-subsamples-output-file' is given, the script
+will generate another file with tubes definitions where each tube is
+produced appliying a specific laboratory protocol to an existing
+tube. Existing tubes are the ones in tubes-out-file, new tubes' labels
+are created using the pattern **tube_label::protocol**
+The config_parameters field must point to a YAML configuration file
+with the following structure:
+
+  config_parameters:
+    study_label: study_label
+    
+    namespace: namespace
+
+where study_label is mandatory
+  </help>
+</tool>
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