--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selectproteinids.xml	Tue Jul 03 17:34:13 2018 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<tool id="selectproteinids" name="Filter ids" version="1.0" hidden="false">
+  
+  <description></description>
+  <command interpreter="perl">
+    selectproteinids.pl $input $maintaincon $out_file
+  </command>
+
+  <inputs>
+    <param format="tabular" name="input" type="data" label="Input table"/>
+
+    <param name="maintaincon" type="select" display="radio" label="Maintain contaminants">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="out_file" label="${input.name} filtered"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="protein_ids_simple.csv"/>
+      <param name="maintaincon" value="yes"/>
+      <output name="out_file" file="proteinGroups_csv_filtered_with_contaminants.tabular"/>
+    </test>
+
+    <test>
+      <param name="input" value="protein_ids_simple.csv"/>
+      <param name="maintaincon" value="no"/>
+      <output name="out_file" file="proteinGroups_csv_filtered_without_contaminants.tabular"/>
+    </test>
+
+  </tests>
+
+  <help>
+
+    Input: Protein Groups from MaxQuant
+
+
+    Output: Table with id's got from MaxQuant Protein Groups
+
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @misc{Concatenate,
+        author = {Application, Labis},
+        year = 2018,
+        title = Concatenate,
+        publisher = labisapplications
+      }
+    </citation>
+  </citations>
+</tool>