--- a/deconrank.xml	Thu Oct 12 11:21:34 2017 -0400
+++ b/deconrank.xml	Tue Mar 27 07:18:42 2018 -0400
@@ -1,13 +1,14 @@
-<tool id="deconrank" name="deconrank" version="0.1.0">
+<tool id="deconrank" name="deconrank" version="0.3.4">
     <description>Deconvolute adducts and isotopes then score and rank for fragmentation</description>
     <requirements>
-        <requirement type="package" version="0.0.2">deconrank</requirement>
+        <requirement type="package" version="0.0.26">deconrank</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
 
     <command ><![CDATA[
+        echo "$irm" &&
         python -m deconrank
                     -i $peaks_file
                     -o .
@@ -33,7 +34,14 @@
                     #if $full_output
                         --full_output
                     #end if
-    ]]></command>
+                    #if $dschedule.template_cond.template_select == "user"
+                        --method_template_name '$dschedule.template_cond.template_name'
+                    #end if
+                    --target_name '$peaks_file.element_identifier'
+
+                    && ls && pwd
+
+     ]]></command>
 
     <inputs>
         <param type="data" name="peaks_file" format="tabular,tsv"
@@ -44,9 +52,7 @@
             <option value="dims">DI-MS</option>
         </param>
 
-        <param name="polarity" type="select" label="polarity" help="polarity [pos, neg], will assign automatically
-                                                                    based on input file name if not defined" >
-            <option value="auto" selected="true">automatic (based on input file name)</option>
+        <param name="polarity" type="select" label="polarity" help="polarity [pos, neg]" >
             <option value="pos" >positive</option>
             <option value="neg">negative</option>
         </param>
@@ -109,26 +115,38 @@
             <param name="percentage_cid" type="float" value="0.333" min="0" max="1" help="Percentage of time fragmenting using
                                                             CID (rather than HCD)"/>
             <param name="delay_time" type="float" value="24" help="Delay time before acquisition begins (secs)"/>
+
+            <conditional name="template_cond">
+                <param name="template_select" type="select" label="Use default method template file names?"
+                  help="Default names are: Neg_MSMS_MSn.meth and Pos_MSMS_MSn.meth">
+                    <option value="default" >Default</option>
+                    <option value="user" >Provide name</option>
+                </param>
+                <when value="user">
+                         <param name="template_name" label="method template name" type="text" />
+                </when>
+                <when value="default"> </when>
+            </conditional>
         </section>
 
 
-
     </inputs>
     <outputs>
-        <data name="decon_scores" label="${tool.name} on ${on_string}: scores"
+        <data name="scores" label="${tool.name} on ${on_string}: scores"
               from_work_dir="scores.tsv"  format="tsv"/>
-        <data name="decon_traceback" label="${tool.name} on ${on_string}: traceback"
+        <data name="traceback" label="${tool.name} on ${on_string}: traceback"
               from_work_dir="traceback.tsv" format="tsv"/>
-        <data name="decon_xcalibur_auto_input" label="${tool.name} on ${on_string}: XcaliburAuto input"
-              from_work_dir="XcaliburAutoInput.tsv" format="tsv">
+
+        <collection name="targets"  type="list" label="${tool.name} on ${on_string}: targets" format="tsv">
+              <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv"  directory="targets"   format="tsv" visible="false"
+              assign_primary_output="true"/>
+              <filter>technology == "dims"</filter>
+        </collection>
+
+        <data name="XcaliburAutoInput" label="${tool.name} on ${on_string}: XcaliburAutoInput"
+              from_work_dir="xcalibur_auto_input.tsv" format="tsv">
             <filter>technology == "dims"</filter>
         </data>
-        <data name="decon_targets" label="${tool.name} on ${on_string}: targets"
-              from_work_dir="target.tsv" format="tsv">
-            <filter>technology == "dims"</filter>
-        </data>
-
-
 
     </outputs>
     <tests>
@@ -136,10 +154,10 @@
             <param name="peaks_file" value="camera_annotated_peaklist.txt" ftype="tsv"/>
             <param name="technology" value="dims"/>
             <param name="polarity" value="pos"/>
-            <output name="decon_scores" value="scores.tsv"/>
-            <output name="decon_traceback" value="traceback.tsv"/>
-            <output name="decon_xcalibur_auto_input" value="XcaliburAutoInput.tsv"/>
-            <output name="decon_targets" value="target.tsv"/>
+            <output name="scores" value="scores.tsv"/>
+            <output name="traceback" value="traceback.tsv"/>
+            <output name="XcaliburAutoInput" value="XcaliburAutoInput.tsv"/>
+            <output name="target" value="target.tsv"/>
         </test>
     </tests>
 
@@ -148,4 +166,4 @@
 
     ]]></help>
     <citations>    </citations>
-</tool>
\ No newline at end of file
+</tool>