--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pecan2blib.xml	Fri Aug 25 14:25:21 2017 -0400
@@ -0,0 +1,38 @@
+<tool id="pecan2blib" name="pecan2blib" version="0.1.0">
+    <description>Convert PECAN results after percolator (.peptides) into spectral library (.blib)</description>
+    <requirements>
+        <requirement type="package" version="0.9.9.3">pecan</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        pecan2blib -o pecan_spectral_lib --ionTypes=$ionTypes -q $qValue $toMinutes 
+        #if $extension and str($extension):
+            -e $extension
+        #end if
+        -l $percolator_results
+        && cat "pecan_spectral_lib"*.blib > '$spectral_lib'
+    ]]></command>
+    <inputs>
+        <param name="percolator_results" type="data" format="percout" multiple="true" label="percolator results"/>
+        <param name="ionTypes" type="select" label="Fragment ion types" help="suggested HCD: y, reCID: by">
+            <option value="by">by</option>
+            <option value="y">y</option>
+            <option value="b">b</option>
+        </param>
+        <param name="qValue" type="float" value="0.01" label="q-value threshold"/>
+        <param name="toMinutes" type="boolean" truevalue="--toMinutes" falsevalue="" checked="false" 
+           label="Convert retention time from seconds to minutes"
+           help="Only needed when mzML files recorded retention time in seconds"/>
+        <param name="extension" type="text" value="" optional="true" label="raw file extension for skyline"
+            help="original file extension (e.g. raw/wiff) for proper Skyline views"/>
+
+    </inputs>
+    <outputs>
+        <data name="spectral_lib" format="sqlite" />
+    </outputs>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+</tool>