diff galaxy-tools/biobank/utils/prepare_seq_out_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_out_inputs.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,46 @@
+<tool id="vl_prepare_seq_out_inputs"
+      name="VLUTIL.prepare_seq_out_inputs">
+  <description>
+    Extract OMERO.biobank objects that can be used to import SequencerOutput data
+  </description>
+
+ <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=prepare_seq_out_inputs.py
+    --in-file=${infile}
+    --logfile=${log_file}
+    --dsamples-out-file=${dsamples_ofile}
+    --dobjects-out-file=${dobjects_ofile}
+    --study=${study}
+  </comand>
+
+  <inputs>
+    <param format="tabular" name="infile" type="data"
+      label="Input file (in TAB-separated format)"/>
+    <param name="study" size="40" type="text" label="Study label"/>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="dsamples_ofile"
+      label="${tool.name}_dsamples.tsv"/>
+    <data format="tabular" name="dobjects_ofile"
+      label="${tool.name}_dobjects.tsv"/>
+    <data format="txt" name="log_file"
+      label="${tool.name}.log"/>
+  </outputs>
+
+  <help>
+This tool produces files that can be used as input to import
+ * SequencerOutput data samples
+ * SequencerOutput data objects
+within OMERO.biobank using import applications.
+
+Input file must be like
+
+ run_directory                   path
+ 130418_SN194_0303_BC1NYHACXX    file:///SHARE/USERFS/els7/users/sequencing_data/completed/130418_SN194_0303_BC1NYHACXX/raw
+ 160418_SN194_0304_BCAZYHACXX    file:///SHARE/USERFS/els7/users/sequencing_data/completed/160418_SN194_0304_BCAZYHACXX/raw
+ ....
+  </help>
+</tool>
\ No newline at end of file