--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlibToMs2.xml	Tue May 08 14:16:45 2018 -0400
@@ -0,0 +1,73 @@
+<tool id="BlibToMs2" name="BlibToMs2" version="@VERSION@.0">
+    <description>convert spectrum library blib to MS2 format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        BlibToMs2   
+        --mz-precision $mz_precision
+        --intensity-precision $intensity_precision
+        --mod-precision $mod_precision
+        -f '$output'   
+        '$blib'
+    ]]></command>
+    <inputs>
+        <param name="blib" type="data" format="sqlite" label="Blib to convert to MS2"/>
+        <param name="mz_precision" type="integer" value="2" min="1" max="6"
+            label="Precision for peak m/z printed to ms2"
+            help="--mz-precision"/>
+        <param name="intensity_precision" type="integer" value="1" min="1" max="6"
+            label="Precision for peak intensities printed to ms2"
+            help="--intensity-precision"/>
+        <param name="mod_precision" type="integer" value="1" min="1" max="6"
+            label="Precision for modification masses"
+            help="--mod-precision"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="ms2" label="${blib.name.rsplit('.',1)[0]}.ms2"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" />
+                    <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries.
+
+BlibToMs2_ creates a library of peptide MS/MS spectra from a variety of different database search results. 
+
+::
+
+  Usage: BlibToMs2 [options] <library>
+  
+  Options:
+    -f [ --file-name ] arg                Name the output ms2 file.  Default is 
+                                          <library name>.ms2.
+    -m [ --mz-precision ] arg (=2)        Precision for peak m/z printed to ms2. 
+                                          Default 2.
+    -i [ --intensity-precision ] arg (=1) Precision for peak intensities.  
+                                          Default 1.
+    -p [ --mod-precision ] arg (=-1)      Precision for modification masses.  
+                                          Default -1 (use value in PeptideModSeq 
+                                          column).
+    -p [ --parameter-file ] arg           File containing search parameters.  
+                                          Command line values override file 
+                                          values.
+    -v [ --verbosity ] arg (=status)      Control the level of output to stderr. 
+                                          (silent, error, status, warn, debug, 
+                                          detail, all)  Default status.
+    -h [ --help ]                         Print help message.
+
+
+.. _BlibToMs2: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibToMs2
+.. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
+    ]]></help>
+    <expand macro="citations" />
+</tool>