--- a/msgfplus_search.xml	Thu Jun 26 11:39:21 2014 -0400
+++ b/msgfplus_search.xml	Thu Mar 26 20:04:30 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
+<tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
     <description>Run an MSGF+ Search</description>
     <requirements>
-        <requirement type="package" version="1.3">protk</requirement>
+        <container type="docker">iracooke/protk-1.4.1</container>
+        <requirement type="package" version="1.4">protk</requirement>
         <requirement type="package" version="20140210">msgfplus</requirement>
         <requirement type="package" version="3_0_4388">proteowizard</requirement>
     </requirements>
@@ -45,6 +46,9 @@
         --min-pep-charge=$min_pep_charge
         --num-reported-matches=$num_reported_matches
         --java-mem=$java_mem
+
+        --threads $threads
+
         #if $pepxml_output_use:
         --pepxml
         #end if
@@ -94,7 +98,7 @@
             <label>Missed Cleavages Allowed</label>
             <option value="0">0</option>
             <option value="1">1</option>
-            <option value="2">2</option>
+            <option selected="true" value="2">2</option>
         </param>
         
         <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
@@ -116,7 +120,7 @@
         <param name="instrument" type="select" format="text">
             <label>Instrument Type</label>
             <option value="2">TOF</option>
-            <option value="0">Low-res LCQ/LTQ</option>
+            <option value="0" selected="true">Low-res LCQ/LTQ</option>
             <option value="1">High-res LTQ</option>
         </param>
 
@@ -137,7 +141,7 @@
             <option value="3">iTRAQPhospho</option>
         </param>
 
-        <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
+        <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
         <param name="precursor_tolu" type="select" format="text">
             <label>Precursor Ion Tolerance Units</label>
             <option value="ppm">ppm</option>
@@ -151,24 +155,33 @@
         <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
         <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
         <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
-        <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
+        <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>        
+        <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
     </inputs>
     <outputs>
-        <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}">
+        <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.${'pepXML' if $pepxml_output_use else 'mzid'}">
             <change_format>
-                <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" 
-                    label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
+                <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
             </change_format>
         </data>
     </outputs>
+
     <tests>
+        <!-- Just test that the tool runs and produces vaguely correct output -->
         <test>
             <param name="source_select" value="input_ref"/>
-              <param name="fasta_file" value="bsa.fasta"/>
-                  <param name="input_file" value="bsa.mzML"/>
-              <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> 
+            <param name="fasta_file" value="testdb.fasta" format="fasta"/>
+            <param name="input_file" value="tiny.mzML" format="mzml"/>
+            <param name="precursor_ion_tol" value="200"/>
+            <param name="pepxml_output_use" value="true"/>
+            <output name="output" format="raw_pepxml">
+                <assert_contents>
+                    <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
+
     <help>
 
 **What it does**