changeset 7:975b05518cb9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/study.xml	Thu Sep 22 08:28:53 2016 -0400
@@ -0,0 +1,83 @@
+<tool id="vl_import_study" name="VLI.study">
+  <description>import study definitions within omero/vl</description>
+  <command interpreter="python">
+    #if $__app__.config.vl_import_enabled_users.split(',').count($__user_email__)==1 #importer.py
+    #else #unauthorized_access.py
+    #end if
+    #if $advanced_configuration.configuration_level == 'advanced'
+      --host=$advanced_configuration.vl_host
+      --user=$advanced_configuration.vl_user
+      --passwd=$advanced_configuration.vl_passwd
+    #end if
+    --operator=galaxy
+    --ifile=$input
+    --ofile=$output
+    --report_file=$report
+    --loglevel=$__app__.config.vl_loglevel
+    --logfile=${logfile}
+    #if $blocking_validation
+      --blocking-validator
+    #end if
+    study
+  </command>  
+
+  <inputs>
+    <param format="tabular" name="input" type="data"
+	   label="A tabular dataset with the following columns ..."/>
+
+    <!-- ************************************************** -->
+    <param name="blocking_validation" type="boolean" checked="false"
+	   label="Blocking validation"
+	   help="When this check is enabled, if at least one record doesn't pass importer's validation, the entire import procedure will be blocked"/>
+
+    <conditional name="wait_for_trigger">
+      <param name="enable_trigger" type="boolean" checked="false"
+	     label="Wait for another tool to end before running this tool"/>
+      <when value="true">
+	<param format="txt" name="trigger_file" type="data"
+	       label="Select the LOG file that will be used as trigger"/>
+      </when>
+    </conditional>   
+
+    <conditional name="advanced_configuration">
+      <param name="configuration_level" type="select" 
+	     label="Configuration level">
+	<option value="default" selected="true">Default configuration</option>	
+	<option value="advanced">Advanced configuration</option>
+      </param>
+      <when value="advanced">
+	<param name="vl_host" size="40" type="text" 
+	       value="localhost" 
+	       label="Omero/VL host"/>
+	<param name="vl_user" size="20" type="text" 
+	       value="root" 
+	       label="Omero/VL user"/>
+	<param name="vl_passwd" size="20" type="text" 
+	       value="What_Me_worry?" 
+	       label="Omero/VL passwd"/>
+      </when>
+      <when/>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" label="${tool.name}.mapping"/>
+    <data format="tabular" name="report" label="${tool.name}.report"/>
+    <data format="txt" name="logfile" label="${tool.name}.logfile"/>
+  </outputs>
+
+  <help>
+Will import a stream of new study definitions defined by the following
+tab-separated columns. A typical file will look like the following::
+
+  label	 description
+  BSTUDY A basically empty description of BSTUDY
+  CSTUDY A basically empty description of CSTUDY
+  ....
+  </help>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+</tool>