diff msconvert_macros.xml @ 16:545054b15d7c draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd

--- a/msconvert_macros.xml	Mon Nov 30 16:01:10 2020 +0000
+++ b/msconvert_macros.xml	Sun Mar 24 11:13:43 2024 +0000
@@ -221,7 +221,7 @@
         && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
       #else
         ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
-        ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
+        ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
         #if $output_type == 'mzML' or $output_type == 'mzXML'
           && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
           ## a newline is needed after `#echo ...` therefore the `;'` on the next line
@@ -251,7 +251,10 @@
 
     <section name="data_processing" title="Data Processing Filters">
         <conditional name="peak_picking">
-            <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
+            <param type="select" name="pick_peaks" label="Apply peak picking?">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
             <when value="false" />
             <when value="true">
                 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
@@ -268,7 +271,10 @@
       </conditional>
 
       <conditional name="precursor_refinement">
-        <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
+        <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
+            <option value="true">Yes</option>
+            <option value="false" selected="true">No</option>
+        </param>
         <when value="false"></when>
         <when value="true">
           <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
@@ -337,7 +343,10 @@
       </repeat>
 
       <conditional name="filter_mz_windows">
-        <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
+        <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
@@ -346,7 +355,10 @@
       </conditional>
 
       <conditional name="etd_filtering">
-        <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
+        <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
@@ -374,7 +386,10 @@
       </conditional>
 
       <conditional name="ms2denoise">
-        <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter"  />
+        <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="true">
           <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
           <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
@@ -386,7 +401,10 @@
       <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
 
       <conditional name="demultiplex">
-        <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
+        <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="true">
           <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
           <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
@@ -397,13 +415,13 @@
           <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
           <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
           <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
-          <param name="noSumNormalize" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Normalize sums" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
+          <param name="noSumNormalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No sum normalization?" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
           <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
             <option value="none" selected="true">None</option>
             <option value="overlap_only">Overlap only</option>
           </param>
           <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
-          <param name="noWeighting" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
+          <param name="noWeighting" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
           <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
         </when>
         <when value="false" />
@@ -443,7 +461,10 @@
       <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
 
       <conditional name="filter_ms_levels">
-        <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
+        <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
@@ -471,7 +492,10 @@
       <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
 
       <conditional name="scan_summing">
-        <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
+        <param name="do_scan_summing" type="select" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false" />
         <when value="true">
           <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
@@ -486,7 +510,10 @@
       <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue=""  label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
 
       <conditional name="multi_run_output">
-        <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
+        <param name="do_multi_run_output" type="select" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)">
+            <option value="true">Yes</option>
+            <option value="false">No</option>
+        </param>
         <when value="false">
           <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
         </when>
@@ -535,7 +562,7 @@
       <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
         <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
       </data>
-      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
+      <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
         <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
         <discover_datasets pattern="__name_and_ext__" directory="outputs" />
       </collection>
@@ -544,7 +571,7 @@
 
 
   <xml name="msconvert_tests">
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -553,7 +580,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.RAW" ftype="thermo.raw" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -562,7 +589,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -570,19 +597,19 @@
       <param name="do_scan_summing" value="true" />
       <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
       <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
       <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -591,7 +618,7 @@
       <param name="pick_peaks_ms_levels" value="1-" />
       <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -599,7 +626,7 @@
       <param name="runIndexSet" value="0" />
       <output name="output" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -610,7 +637,7 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -621,7 +648,7 @@
       <param name="srmAsSpectra" value="true" />
       <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -633,7 +660,7 @@
         <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
       </output_collection>
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -645,7 +672,7 @@
     </test>
 
     <!-- this data file only has profile MS1, so the result is the same -->
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -654,7 +681,7 @@
       <param name="pick_peaks_ms_levels" value="1" />
       <output name="output" file="small-peakpicking-cwt-allMS.mzML" ftype="mzml" lines_diff="8" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mz5" />
@@ -662,7 +689,7 @@
       <param name="intensity_encoding" value="64" />
       <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzXML" />
@@ -690,7 +717,7 @@
       <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
     </test>-->
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -698,7 +725,7 @@
       <output name="output" file="small-numpressLP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -706,7 +733,7 @@
       <output name="output" file="small-numpressLS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -714,7 +741,7 @@
       <output name="output" file="small-numpressL.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -722,7 +749,7 @@
       <output name="output" file="small-numpressP.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -730,7 +757,7 @@
       <output name="output" file="small-numpressS.mzML" ftype="mzml" lines_diff="114" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="Rpal_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -743,7 +770,7 @@
       <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
     </test>
 
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -756,7 +783,7 @@
       <param name="maxKnownCharge" value="8" />
       <output name="output" file="small-chargeStatePredictor.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -771,7 +798,7 @@
       <param name="defaultMaxCharge" value="5" />
       <output name="output" file="small-turbocharger.mzML" ftype="mzml" lines_diff="114" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -785,7 +812,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -798,7 +825,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-threshold.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -808,7 +835,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-mzWindow.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -819,7 +846,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-denoise.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -827,7 +854,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-deisotope.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -835,7 +862,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -848,7 +875,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-index-filter.mzML" lines_diff="32" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -856,7 +883,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-strip-it.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -866,7 +893,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -874,7 +901,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -882,7 +909,7 @@
       <param name="binary_compression" value="numpressLinearPic" />
       <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" ftype="mzml" />
     </test>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
       <param name="license_agreement" value="true" />
       <param name="output_type" value="mzML" />
@@ -902,16 +929,6 @@
       <output name="output" file="small-deisotope-poisson.mzML" />
     </test>-->
   </xml>
-  <xml name="msconvert_help">
-**What it does**
-
-Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
-
-You can view the original documentation here_.
-
-.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
-  </xml>
-
   <xml name="citations">
     <citations>
         <citation type="doi">10.1093/bioinformatics/btn323</citation>