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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/query.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,79 @@
+<tool id="vl_tools_query" name="VLT.query">
+  <description>
+    Provides a simplified environment to perform complex queries to
+    BIOBANK.
+  </description>
+  <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=kb_query.py
+    --host=$__user_omero_host__
+    --user=$__user_omero_user__
+    --passwd=$__user_omero_password__
+    --operator=$__user_email__
+    --ofile=${output1}
+    --logfile=${logfile}
+    query
+    --group=$study
+    --code-file=$code_file
+  </command>  
+  <inputs>
+    <param name="study" type="select" label="study label" 
+	   help="Choose one of the available groups/studies. 
+		 See below.">    
+      <options from_parameter="tool.app.known_studies" 
+	       transform_lines="[ &quot;%s%s%s:%s&quot; 
+				% ( l[0], self.separator, l[0], l[1][:40] ) 
+				for l in obj ]">
+	<column name="value" index="0"/>
+	<column name="name" index="1"/>
+	<filter type="sort_by" column="0"/>
+      </options>
+    </param>
+    <param name="query_code" type="text" area="True" size="10x60" 
+           optional="False"
+           value=""
+	   />
+    <!-- ************************************************** -->
+
+  </inputs>
+
+  <configfiles>
+    <configfile name="code_file">${str($query_code).replace('__sq__', "'").replace('__cr____cn__', '\n')}</configfile>
+  </configfiles>
+
+  <outputs>
+    <data format="tabular" name="output1" label="${tool.name}.mapped"/>
+    <data format="txt" name="logfile"     label="${tool.name}.logfile"/>
+  </outputs>
+
+  <help>
+The following is an example of a query that will dump family relations
+within the group::
+
+   writeheader('study', 'id', 'gender', 'father', 'mother')
+   for i in Individuals(group):
+      writerow(group.id, enum_label(i.gender), 
+               i.father.id if i.father else 'None', 
+               i.mother.id if i.mother else 'None')
+
+
+The next example will prepare a file that could be used to define a
+data collection and then as the input for a genotyping run::
+
+   writeheader('dc_id', 'gender', 'data_sample', 
+               'path', 'mimetype', 'size', 'sha1')
+   for i in Individuals(group):
+      for d in DataSamples(i, 'AffymetrixCel'):
+         for o in DataObjects(d):
+            writerow(group.id, enum_label(i.gender), d.id,
+                     o.path, o.mimetype, o.size, o.sha1)
+
+In the examples above, '''group''' (actually a study) corresponds to
+the group whose label is assigned by the '''--group''' flag.
+
+**Note** This is clearly an extremely dangerous tool.
+    
+  </help>
+
+</tool>
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