--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msconvert_subset.xml	Wed Dec 19 00:10:08 2012 -0500
@@ -0,0 +1,105 @@
+<tool id="msconvert_subset" name="Subset Peak List" version="0.1.0">
+  <description>against list of scan numbers or indices.</description>
+  <command interpreter="python">
+    msconvert_wrapper.py 
+    --input=${input} 
+    --output=${output} 
+    --fromextension=${input.ext} 
+    --toextension=${output_type} 
+    #if $settings.settingsType == "full"
+    --binaryencoding=${settings.binary_encoding} 
+    --mzencoding=${settings.mz_encoding} 
+    --intensityencoding=${settings.intensity_encoding}
+    --zlib=${settings.zlib}
+    #end if
+    --filter_table="$filter.filterList"
+    #if $filter.filterType == "scan_number"
+    --filter_table_type="number"
+    #else
+    --filter_table_type="index"
+    #end if
+  </command>
+
+  <inputs>
+    <conditional name="type">
+      <param name="input_type" type="select" label="Input Type">
+        <option value="mzml">mzML</option>
+        <option value="mzxml">mzXML</option>
+        <option value="mgf">mgf</option>
+        <option value="ms2">ms2</option>
+      </param>
+      <when value="mzml">
+        <param format="mzml" name="input" type="data" label="Input mzML"/>
+      </when>
+      <when value="mzxml">
+        <param format="mzxml" name="input" type="data" label="Input mzXML"/>
+      </when>
+      <when value="mgf">
+        <param format="mgf" name="input" type="data" label="Input mgf"/>
+      </when>
+      <when value="ms2">
+        <param format="ms2" name="input" type="data" label="Input ms2"/>
+      </when>
+    </conditional>
+    <param name="output_type" type="select" label="Output Type">
+      <option value="mzML">mzML (indexed)</option>
+      <option value="unindexed_mzML">mzML (unindexed)</option>
+      <option value="mzXML">mzXML (indexed)</option>      
+      <option value="unindexed_mzXML">mzXML (unindexed)</option>
+      <option value="mgf">mgf</option>
+      <option value="ms2">ms2</option>  
+    </param>
+    <conditional name="filter">
+      <param name="filterType" type="select" label="Filter by" help="">
+        <option value="scan_number" selected="true">Scan Number</option>
+        <option value="scan_index">Scan Index</option>
+      </param>    
+      <when value="scan_number">
+        <param format="text" name="filterList" type="data" label="Scan Numbers"/>
+      </when>
+      <when value="scan_index">
+        <param format="text" name="filterList" type="data" label="Scan Indices"/>
+      </when>
+    </conditional>
+    <conditional name="settings">
+      <param name="settingsType" type="select" label="Advanced msconvert Settings" help="">
+        <option value="default">Use Defaults</option>
+        <option value="full">Full Parameter List</option>
+      </param>
+      <when value="default" />
+      <when value="full">
+        <param type="select" name="binary_encoding" label="Binary Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="mz_encoding" label="m/z Encoding Precision">
+          <option value="64" selected="true">64</option>
+          <option value="32">32</option>
+        </param>
+        <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
+          <option value="64">64</option>
+          <option value="32" selected="true">32</option>
+        </param>
+        <param type="boolean" name="zlib" label="Use zlib">      
+        </param>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="output">
+      <change_format>
+        <when input="output_type" value="mzXML" format="mzxml" />
+        <when input="output_type" value="unindexed_mzXML" format="mzxml" />
+        <when input="output_type" value="ms2" format="ms2" />
+        <when input="output_type" value="mgf" format="mgf" />
+      </change_format>
+    </data>
+  </outputs>
+
+  <requirements>
+    <requirement type="package">proteowizard</requirement>    
+  </requirements>
+
+  <help>
+  </help>
+</tool>