--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectrast_filter.xml	Thu Mar 29 09:51:50 2018 -0400
@@ -0,0 +1,65 @@
+<tool id="spectrast_filter_1" name="SpectraST Filter" version="5.0.0">
+    <description>Filter and Manipulate Spectral Libraries</description>
+    <requirements>
+        <!--
+        <container type="docker">iracooke/protk-1.4.3</container>
+        -->
+        <requirement type="package" version="1.4.4a">protk</requirement>
+        <requirement type="package" version="5.0.0">tpp</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Job Failed" />
+    </stdio>
+    <command>
+<![CDATA[
+        spectrast_filter.rb  --merge $merge
+
+        #for $splib_file in $splib_files:
+            ${splib_file.extra_files_path}/library.splib
+        #end for
+
+        --replicates $replicates
+        -o library
+
+        &&
+
+        mkdir -p ${output.files_path}
+
+        &&
+
+        cp library.splib library.spidx library.pepidx  ${output.files_path}/
+
+        &&
+
+        echo "Spectral Library Primary File" > $output
+]]>
+    </command>
+    <inputs>
+        <param name="splib_files" multiple="true" type="data" format="splib" label="Spectral Libraries to operate on" help=""/>
+        <param name="merge" type="select" format="text">
+            <label>Merge Method</label>
+            <option value="U">Union</option>
+            <option value="S">Subtraction</option>
+            <option value="H">Subtraction of homologs</option>
+            <option value="A">Appending</option>
+        </param>
+
+        <param name="replicates" type="select" format="text">
+            <label>How to deal with replicate spectra</label>
+            <option value="None">Keep All</option>
+            <option value="C">Consensus</option>
+            <option value="B">Best replicate</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="splib" name="output"/>
+    </outputs>
+    <help>
+<![CDATA[
+**What it does**
+
+Filter and Manipulate Spectral Libraries
+
+]]>
+    </help>
+</tool>