add option for additonal output files, state and transition matrices

mudirac/mudirac.xml

@@ -21,6 +21,7 @@ isotope: $isotope
 xr_lines: $xr_lines
 uehling_correction: $uehling_correction
 nuclear_model: $nuclear_model
+output: $output_level
 #if $electronic_config:
 electronic_config: $electronic_config
 #end if</configfile>
@@ -163,9 +164,21 @@ electronic_config: $electronic_config
         <param name="uehling_correction" type="boolean" value="false" label="Uehling correction" help="whether to turn on the Uehling correction or not" optional="true"/>
         <param name="electronic_config" type="text" value="" label="electronic configuration to use in order to describe the negative charge background" help="Can be a full string describing the configuration (e.g. 1s2 2s2 2p2), 
         an element symbol to represent the default configuration of that atom when neutral (e.g. C) or a mix of the two (e.g. [He] 2s2 2p2)" optional="true"/>
+        <param name="output_level" type="select" label="ouput level">
+            <option value="1" selected="true"> Only transition energies and rates</option>
+            <option value="2"> Transiion energies, states and transition matrices</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="tabular" label="Output of ${tool.name}" from_work_dir="input.xr.out"/>
+        <collection name="states" format="tabular" label="States" type="list">
+            <filter>output_level=="2"</filter>
+            <discover_datasets pattern="(input)\.(?P&lt;designation&gt;[KLMNOPQ]\d).out" format="tabular" visible="true" />
+        </collection>
+        <collection name="transition_matrices" format="tabular" label="Transition matrices" type="list">
+            <filter>output_level=="2"</filter>
+            <discover_datasets pattern="(input)\.(?P&lt;designation&gt;[KLM]\d-[KLM]\d).tmat.out" format="tabular" visible="true" />
+        </collection>
         <data name="log_out" label="log file of ${tool.name}" format="txt" from_work_dir="input.log"/>
         <data name="error_log" label="Error log file of ${tool.name}" format="txt" from_work_dir="input.err"/>
     </outputs>