--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BlibFilter.xml	Tue May 08 14:16:45 2018 -0400
@@ -0,0 +1,76 @@
+<tool id="BlibFilter" name="BlibFilter" version="@VERSION@.0">
+    <description>remove redundant spectra from a library</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        BlibFilter 
+        --min-peaks $min_peaks
+        --min-score $min_score
+        --best-scoring $best_scoring
+        '$redundant_blib' '$filtered_blib'
+        #if $convert_to_ms2:
+            && BlibToMs2 -f '$ms2' '$filtered_blib'
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="redundant_blib" type="data" format="sqlite" label="Redundant Blib"/>
+        <param name="min_peaks" type="integer" value="1" min="1" 
+            label="Only include spectra with at least this peaks"
+            help="--min-peaks"/>
+        <param name="min_score" type="float" value="0" min="0"
+            label="Best spectrum must have at least this average score to be included."
+            help="--min-score"/>
+        <param name="best_scoring" type="boolean" truevalue="1" falsevalue="0" checked="false"
+            label="Use best scoring"/>
+        <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/>
+    </inputs>
+    <outputs>
+        <data name="filtered_blib" format="sqlite" label="Filtered Blib"/>
+        <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" >
+            <filter>convert_to_ms2 == True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="redundant_blib" ftype="sqlite" value="msgf.blib"/>
+            <param name="convert_to_ms2" value="True"/>
+            <output name="ms2">
+                <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.
+
+BlibFilter_ creates a library of peptide MS/MS spectra from a variety of different database search results. 
+
+::
+
+  Usage: BlibFilter [options] <redundant-library> <filtered-library>
+
+  Options:
+    -m [ --memory-cache ] arg (=250)  SQLite memory cache size in Megs.  Default
+                                      250M.
+    -n [ --min-peaks ] arg (=1)       Only include spectra with at least this
+                                      many peaks.  Default 1.
+    -s [ --min-score ] arg (=0)       Best spectrum must have at least this
+                                      average score to be included.  Default 0.
+    -b [ --best-scoring ] arg (=0)    Description of option.  Default false.
+    -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.
+  
+
+.. _BlibFilter: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibFilter
+.. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view?
+    ]]></help>
+    <expand macro="citations" />
+</tool>