--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_psms.xml	Mon Dec 21 23:43:55 2015 -0500
@@ -0,0 +1,99 @@
+<tool id="filter_psms" name="Filter PSMs" version="1.0.0">
+	<description>Select PSMs in a pepXML file matching criteria</description>
+
+	<requirements>
+	    <requirement type="package" version="1.4">protk</requirement>
+   </requirements>
+
+	<command>
+		filter_psms.rb 
+
+		'
+		$first_expression
+    #for $expression in $expressions:
+    ,${expression.expression}
+    #end for
+    '
+
+    $pepxml_file
+
+    --attribute $attribute
+
+    $check_alt
+
+    $reverse
+
+		-o $output
+
+
+	</command>
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+
+		<param name="pepxml_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Proteomics Search Results" help="A pepXML file"/>
+
+
+        <param name="first_expression" type="text" size="40" value="decoy_" label="Expression">
+	    	<sanitizer>
+        	<valid initial="string.printable">
+         	<remove value="&apos;"/>
+        	</valid>
+        	<mapping initial="none">
+          	<add source="&apos;" target="__sq__"/>
+        	</mapping>
+      		</sanitizer>            	
+        </param>
+
+        <repeat name="expressions" title="Expressions to Match against" help="These can include regular expressions">
+            <param name="expression" type="text" size="40" value="decoy_" label="Expression">
+		    	<sanitizer>
+	        	<valid initial="string.printable">
+	         	<remove value="&apos;"/>
+	        	</valid>
+	        	<mapping initial="none">
+	          	<add source="&apos;" target="__sq__"/>
+	        	</mapping>
+	      		</sanitizer>            	
+            </param>
+        </repeat>
+
+		<param name="attribute" type="text" size="40" value="protein" label="Attribute to use for filtering" help="Must be an attribute of a pepXML search_hit node. For example, protein or peptide">
+	    	<sanitizer>
+        	<valid initial="string.printable">
+         	<remove value="&apos;"/>
+        	</valid>
+        	<mapping initial="none">
+          	<add source="&apos;" target="__sq__"/>
+        	</mapping>
+      		</sanitizer>            	
+        </param>
+
+        <param name="reverse" type="boolean" label="Keep mismatches instead of matches" truevalue="--reject" falsevalue="" />
+
+        <param name="check_alt" type="boolean" label="Check alternative_protein entries" truevalue="--check-alternatives" falsevalue="" help="Also apply the search filter to the protein attribute of alternative_protein entries under each search_hit. A match to any counts as a match."/>
+
+	</inputs>
+
+	<outputs>
+		<data format="pepxml" name="output" />
+	</outputs>
+
+
+  <help>
+
+**What it does**
+
+Filters PSMs in a pepXML file keeping only those that match filtering criteria
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>

--- a/tool_dependencies.xml	Tue Oct 20 20:34:50 2015 -0400
+++ b/tool_dependencies.xml	Mon Dec 21 23:43:55 2015 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="protk" version="1.4.3">
-        <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="991797b02976" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>	
     <package name="blast+" version="2.2.29">
         <repository changeset_revision="0b75bc235e70" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />