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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/gdoize_ms.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,46 @@
+<tool id="vl_tools_gdoize_ms" name="VLUTILS.gdoize_ms">
+  <description>
+    Build missing GDOs for the selected markers set
+  </description>
+  <requirements>
+    <requirement type="package">py_protobuff_cpp</requirement>
+  </requirements>
+  <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=gdoize_ms
+    --logfile=${logfile}
+    #if str($mset_label) != 'select_one'
+      --markers-set-label=$mset_label
+    #end if
+    #if str($study) != 'select_one'
+      --study-label=$study
+    #end if
+    --host=$__user_omero_host__
+    --user=$__user_omero_user__
+    --passwd=$__user_omero_password__
+  </command>
+  <inputs>
+    <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="select_one" selected="true">Select a study</option>
+    </param>
+
+    <param name="mset_label" type="select" label="SNP Markers Set"  ajax = "True" ajax-source = "galaxy/get/snp_marker_sets" sort="True"
+	   help="Choose one of the already defined SNP Markers set.">
+      <option value="select_one" selected="true">Select a SNP markers set</option>
+    </param>
+    
+    <!-- ************************************************** -->
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="logfile" label="${tool.name}.log"/>
+  </outputs>
+
+  <help>
+Iterate over all genotype data samples corresponding to the given
+marker set; create a GDO table row for each genotpye data sample that
+does not already have one.
+  </help>
+</tool>
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