--- a/msconvert_macros.xml	Wed Dec 07 17:43:19 2016 -0500
+++ b/msconvert_macros.xml	Mon Dec 12 17:07:11 2016 -0500
@@ -1,50 +1,26 @@
 <macros>
-  <xml name="generic_requirements">
-    <requirements>
-      <requirement type="package" version="3.0.9016">proteowizard</requirement>
-    </requirements>
-  </xml>
-  <token name="@VERSION@">3.0</token>
-  
   <xml name="msconvertCommand">
-    <command interpreter="python">
+    <command>
 <![CDATA[
-    #import re
-    #set $ext = $input.ext
-    msconvert_wrapper.py
-    #if $ext == 'wiff':
-      #set basename = 'absciex'
-      #if hasattr($input, 'display_name')
-        #set basename = $re.sub('\W','_',$input.display_name)
-      #end if
-      --input=${input.extra_files_path}/wiff
-      --input_name='${basename}.wiff
-      --implicit=${input.extra_files_path}/wiff_scan
-      --input=${input.extra_files_path}/wiff_scan
-      --input_name='${basename}.wiff.scan
-    #else
-      --input=${input}
-      #if hasattr($input, 'display_name')
-      --input_name='${input.display_name}'
-      #end if
+    #set $output_type_str = str($output_type)
+    #set $input_name = $input.display_name
+    #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
+    ln -s '$input' '${input_name}' &&
+
+    #if $data_processing.precursor_refinement.use_mzrefinement
+      #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
+      ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
     #end if
-    --output=${output}
-    ## BEGIN_VERSION_DEFAULT
-    --fromextension=$ext
-    ## END_VERSION_DEFAULT
-    --toextension=${output_type}
+
+    mkdir outdir &&
+    msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'
 
     ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
+      #if $data_processing.peak_picking.pick_peaks
+      --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
+      #end if
+
       #if $data_processing.precursor_refinement.use_mzrefinement
-        #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name)
-        #if $data_processing.precursor_refinement.input_ident.ext == 'mzid':
-          #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name)
-        #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml':
-          #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
-        #end if
-      --ident=$data_processing.precursor_refinement.input_ident
-      --ident_name=$input_ident_name
-      --refinement=$output_refinement
       --filter "mzRefiner $input_ident_name
         msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
         thresholdScore=$data_processing.precursor_refinement.thresholdScore
@@ -53,10 +29,6 @@
         maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
       #end if
 
-      #if $data_processing.peak_picking.pick_peaks
-      --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
-      #end if
-
       #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
       --filter "chargeStatePredictor
         overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
@@ -138,7 +110,6 @@
       #end if
       
     ## OUTPUT ENCODING
-      -- 
       #set $mz_encoding = str($settings.mz_encoding)
       #set $intensity_encoding = str($settings.intensity_encoding)
       #if $mz_encoding == $intensity_encoding
@@ -171,6 +142,14 @@
       --gzip
       #end if
 
+      &&
+
+    #if $data_processing.precursor_refinement.use_mzrefinement
+      mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
+    #end if
+
+    mv 'outdir/$output_name' output &&
+    rmdir outdir
 ]]>
     </command>
   </xml>
@@ -322,14 +301,14 @@
         <option value="CID">CID</option>
         <option value="SA">SA</option>
         <option value="HCD">HCD</option>
-        <option value="BIRD">BIRD</option>
-        <option value="ECD">ECD</option>
-        <option value="IRMPD">IRMPD</option>
-        <option value="PD">PD</option>
-        <option value="PSD">PSD</option>
-        <option value="PQD">PQD</option>
-        <option value="SID">SID</option>
-        <option value="SORI">SORI</option>
+        <option>BIRD</option>
+        <option>ECD</option>
+        <option>IRMPD</option>
+        <option>PD</option>
+        <option>PSD</option>
+        <option>PQD</option>
+        <option>SID</option>
+        <option>SORI</option>
       </param>
 
       <repeat name="indices" title="Filter Scan Indices">
@@ -394,7 +373,7 @@
   
   <xml name="msconvertOutput">
     <outputs>
-      <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
+      <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
         <change_format>
           <when input="output_type" value="mz5" format="mz5" />
           <when input="output_type" value="mzXML" format="mzxml" />
@@ -402,274 +381,9 @@
           <when input="output_type" value="mgf" format="mgf" />
         </change_format>
       </data>
-      <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
+      <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
         <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
       </data>
     </outputs>
   </xml>
-
-
-  <xml name="msconvert_tests">
-    <test>
-      <param name="input" value="small.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="pick_peaks" value="true" />
-      <param name="pick_peaks_algorithm" value="cwt" />
-      <param name="pick_peaks_ms_levels" value="1-" />
-      <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
-    </test>
-
-    <!-- this data file only has profile MS1, so the result is the same -->
-    <test>
-      <param name="input" value="small.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="pick_peaks" value="true" />
-      <param name="pick_peaks_algorithm" value="cwt" />
-      <param name="pick_peaks_ms_levels" value="1" />
-      <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> 
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mz5" />
-      <param name="mz_encoding" value="64" />
-      <param name="intensity_encoding" value="64" />
-      <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzXML" />
-      <param name="mz_encoding" value="32" />
-      <param name="intensity_encoding" value="32" />
-      <output name="output" file="small-zlib-32.mzXML" />
-    </test>
-    <!-- TODO: how to test gzipped output?
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzXML" />
-      <param name="mz_encoding" value="32" />
-      <param name="intensity_encoding" value="32" />
-      <param name="binary_compression" value="false" />
-      <param name="gzip_compression" value="true" />
-      <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="mz_encoding" value="32" />
-      <param name="intensity_encoding" value="32" />
-      <param name="binary_compression" value="false" />
-      <param name="gzip_compression" value="true" />
-      <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
-    </test>-->
-
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-numpressLP.mzML" />
-    </test>
-
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearSlof" />
-      <output name="output" file="small-numpressLS.mzML" />
-    </test>
-
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinear" />
-      <output name="output" file="small-numpressL.mzML" />
-    </test>
-
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressPic" />
-      <output name="output" file="small-numpressP.mzML" />
-    </test>
-
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressSlof" />
-      <output name="output" file="small-numpressS.mzML" />
-    </test>
-
-    <test>
-      <param name="input" value="Rpal_01.mz5" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <param name="use_mzrefinement" value="true" />
-      <param name="input_ident" value="Rpal_01.pepXML.gz" />
-      <param name="thresholdScore" value="mvh" />
-      <param name="thresholdValue" value="40-" />
-      <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
-      <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
-    </test>
-    
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <param name="charge_state_calculation_method" value="predictor" />
-      <param name="predictor_overrideExistingCharge" value="true" />
-      <param name="minMultipleCharge" value="2" />
-      <param name="maxMultipleCharge" value="5" />
-      <param name="singleChargeFractionTIC" value="0.95" />
-      <param name="maxKnownCharge" value="8" />
-      <output name="output" file="small-chargeStatePredictor.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <param name="charge_state_calculation_method" value="turbocharger" />
-      <param name="minCharge" value="1" />
-      <param name="maxCharge" value="5" />
-      <param name="precursorsBefore" value="1" />
-      <param name="precursorsAfter" value="1" />
-      <param name="halfIsoWidth" value="1.5" />
-      <param name="defaultMinCharge" value="1" />
-      <param name="defaultMaxCharge" value="5" />
-      <output name="output" file="small-turbocharger.mzML" />
-    </test>
-    <test>
-      <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
-      <param name="output_type" value="mzML" />
-      <param name="do_etd_filtering" value="true" />
-      <param name="remove_precursor" value="true" />
-      <param name="remove_charge_reduced" value="true" />
-      <param name="remove_neutral_loss" value="false" />
-      <param name="blanket_removal" value="false" />
-      <param name="matching_tolerance" value="50" />
-      <param name="matching_tolerance_units" value="ppm" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="thresholds_0|threshold_type" value="count" />
-      <param name="thresholds_0|value" value="100" />
-      <param name="thresholds_0|orientation" value="most-intense" />
-      <param name="thresholds_1|threshold_type" value="absolute" />
-      <param name="thresholds_1|value" value="1" />
-      <param name="thresholds_1|orientation" value="most-intense" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-threshold.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="do_mzwindow_filter" value="true" />
-      <param name="mz_window_from" value="420" />
-      <param name="mz_window_to" value="840" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-mzWindow.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="denoise" value="true" />
-      <param name="num_peaks" value="10" />
-      <param name="window_width" value="40" />
-      <param name="relax" value="false" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-denoise.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="ms2deisotope" value="true" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-deisotope.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="activation" value="CID" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-activation.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="indices_0|from" value="2" />
-      <param name="indices_0|to" value="4" />
-      <param name="indices_1|from" value="10" />
-      <param name="indices_1|to" value="10" />
-      <param name="indices_2|from" value="13" />
-      <param name="indices_2|to" value="15" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-index-filter.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="strip_it" value="true" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-strip-it.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="do_ms_level_filter" value="true" />
-      <param name="ms_level_from" value="2" />
-      <param name="ms_level_to" value="2" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-ms-level-filter.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="polarity" value="positive" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-polarity-filter.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="analyzer" value="IT" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-analyzer-filter.mzML" />
-    </test>
-    <test>
-      <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="scan_numbers_0|from" value="3" />
-      <param name="scan_numbers_0|to" value="5" />
-      <param name="scan_numbers_1|from" value="11" />
-      <param name="scan_numbers_1|to" value="11" />
-      <param name="scan_numbers_2|from" value="14" />
-      <param name="scan_numbers_2|to" value="16" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
-    </test>
-    <!--<test>
-      <param name="input" value="small.mzML" />
-      <param name="output_type" value="mzML" />
-      <param name="binary_compression" value="numpressLinearPic" />
-      <output name="output" file="small-deisotope-poisson.mzML" />
-    </test>-->
-  </xml>
-  <xml name="msconvert_help">
-**What it does**
-
-Allows interconversion within various mass spectrometry peak list 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>
-        <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
-                                      year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
-    </citations>
-  </xml>
-
 </macros>