--- a/moff.xml	Fri Jan 05 12:47:36 2018 -0500
+++ b/moff.xml	Thu Jan 18 00:51:56 2018 -0500
@@ -1,7 +1,7 @@
 <tool id="proteomics_moff" name="moFF" version="@VERSION@">
     <description>extracts MS1 intensities from spectrum files</description>
     <macros>
-        <token name="@VERSION@">1.2</token>
+        <token name="@VERSION@">1.2.1</token>
         <!-- xml macros, used for shared Galaxy parameter inputs -->
         <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">
         <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff -->
@@ -176,15 +176,13 @@
                --rt_p $task.rt_p
                --rt_p_match $task.rt_p_match
                --output_folder ./out
-               --ext txt
                #if $task.peptide_summary:
                    --peptide_summary 1
                #end if
            &&
            #if $task.peptide_summary:
-               mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' &&
+               mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
            #end if
-           echo -ne
         #end if
     ]]></command>
     <inputs>
@@ -250,13 +248,14 @@
         <!-- test moff_all -->
         <test>
             <param name="task_selector" value="all"/>
-            <param name="input_type_selector" value="ps"/>
+            <param name="ident_input|input_type_selector" value="ps"/>
             <param name="ident_input_file">
                 <collection type="list">
                     <element name="mbr_test1" value="input/mbr_test1.tabular"/>
                     <element name="mbr_test2" value="input/mbr_test2.tabular"/>
                 </collection>
             </param>
+            <param name="msms_input|input_type_selector" value="mzml"/>
             <param name="inputraw">
                 <collection type="list">
                     <element name="mbr_test1" value="input/mbr_test1.mzml"/>
@@ -271,8 +270,16 @@
                 </assert_contents>
             </output>
             <output_collection name="ident_output" type="list">
-                <element name="mbr_test1_match_moff_result" value="output1/mbr_test1_match_moff_result.txt"/>
-                <element name="mbr_test2_match_moff_result" value="output1/mbr_test2_match_moff_result.txt"/>
+                <element name="mbr_test1_match_moff_result">
+                    <assert_contents>
+                        <has_text text="NH2-QVEEAVQSDDK-COOH"/>
+                    </assert_contents>
+                </element>
+                <element name="mbr_test2_match_moff_result">
+                    <assert_contents>
+                        <has_text text="NH2-RDVGINNTVK-COOH"/>
+                    </assert_contents>
+                </element>
             </output_collection>
             <output_collection name="log_output" type="list">
                 <element name="mbr_test1_match__moff">
@@ -290,9 +297,9 @@
         <!-- test moff alone -->
         <test>
             <param name="task_selector" value="moff"/>
-            <param name="input_type_selector" value="ps"/>
+            <param name="ident_input|input_type_selector" value="ps"/>
             <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
-            <param name="msms_input" value="mzml"/>
+            <param name="msms_input|input_type_selector" value="mzml"/>
             <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
             <param name="peptide_summary" value="true"/>
             <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
@@ -305,10 +312,10 @@
         <!-- test the generic input -->
         <test>
             <param name="task_selector" value="moff"/>
-            <param name="input_type_selector" value="generic"/>
+            <param name="ident_input|input_type_selector" value="generic"/>
             <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
             <param name="remove_header" value="true"/>
-            <param name="msms_input" value="mzml"/>
+            <param name="msms_input|input_type_selector" value="mzml"/>
             <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
             <param name="peptide" value="3"/>
             <param name="prot" value="2"/>
@@ -328,7 +335,7 @@
         <!-- test mbr -->
         <test>
             <param name="task_selector" value="mbr"/>
-            <param name="input_type_selector" value="ps"/>
+            <param name="ident_input|input_type_selector" value="ps"/>
             <param name="ident_input_file">
                 <collection type="list">
                     <element name="mbr_test1" value="input/mbr_test1.tabular"/>
@@ -337,8 +344,16 @@
             </param>
             <param name="ext" value="tabular"/>
             <output_collection name="ident_output" type="list" count="2">
-                <element name="mbr_test1_match" file="input/mbr_output/mbr_test1_match.txt"/>
-                <element name="mbr_test2_match" file="input/mbr_output/mbr_test2_match.txt"/>
+                <element name="mbr_test1_match">
+                    <assert_contents>
+                        <has_text text="NH2-QVEEAVQSDDK-COOH"/>
+                    </assert_contents>
+                </element>
+                <element name="mbr_test2_match">
+                    <assert_contents>
+                        <has_text text="NH2-RDVGINNTVK-COOH"/>
+                    </assert_contents>
+                </element>
             </output_collection>
         </test>
     </tests>