--- a/pepquery2.xml	Sun Nov 06 16:25:25 2022 +0000
+++ b/pepquery2.xml	Wed Oct 18 06:40:40 2023 +0000
@@ -33,6 +33,9 @@
 ## PepQuery command
 pepquery 
   -Xmx\$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]g
+#if $digestion.enzyme == '0'
+  -XX:ThreadStackSize=2048
+#end if
 #if $validation.task_type == "known"
   -s 2 $validation.decoy
 #else
@@ -677,6 +680,72 @@
             </output>
         </test>
 
+        <!-- Test-5  Non-enzyme search -->
+        <test expect_num_outputs="2">
+            <conditional name="validation">
+                <param name="task_type" value="novel"/>
+            </conditional>
+            <section name="req_inputs">
+                <conditional name="input_type">
+                    <param name="input_type_selector" value="peptide"/>
+                    <conditional name="multiple">
+                        <param name="peptide_input_selector" value="single" />
+                        <param name="input" value="ELGSSDLTAR"/>
+                    </conditional>
+                </conditional>
+                <conditional name="db_type">
+                    <param name="db_type_selector" value="history" />
+                    <param name="db_file" ftype="fasta" value="Uniprot.fasta"/>
+                </conditional>
+                <conditional name="ms_dataset">
+                    <param name="ms_dataset_type" value="history"/>
+                    <param name="spectrum_files" ftype="mgf" value="iTRAQ_f4.mgf"/>
+                </conditional>
+                <param name="indexType" value="1"/>
+            </section>
+            <param name="parameter_set" value=""/>
+            <section name="modifications">
+                 <!-- 21: iTRAQ 4-plex of K [144.1020624208] -->
+                 <!-- 22: iTRAQ 4-plex of peptide N-term [144.1020624208] -->
+                 <param name="fixed_mod" value="1,21,22"/>
+                 <!-- 2: Oxidation of M [15.99491461956] -->
+                 <param name="var_mod" value="2"/>
+                 <param name="max_mods" value="3"/>
+                 <param name="unmodified" value="True"/>
+                 <param name="aa" value="False"/>
+            </section>
+            <section name="digestion">
+                <param name="enzyme" value="0"/>
+            </section>
+            <section name="ms_params">
+                <section name="tolerance_params">
+                    <param name="precursor_tolerance" value="10"/>
+                    <param name="precursor_unit" value="ppm"/>
+                    <param name="tolerance" value="0.6"/>
+                </section>
+                <section name="search">
+                    <param name="frag_method" value="1"/>
+                    <param name="scoring_method" value="1"/>
+                    <param name="extra_score_validation" value="False"/>
+                    <param name="min_charge" value="2"/>
+                    <param name="max_charge" value="3"/>
+                    <param name="min_peaks" value="10"/>
+                    <param name="isotope_error" value="0"/>
+                    <param name="min_score" value="12"/>
+                    <param name="min_length" value="7"/>
+                    <param name="max_length" value="45"/>
+                    <param name="num_random_peptides" value="1000"/>
+                </section>
+            </section>
+            <output name="psm_rank_txt">
+                <assert_contents>
+                    <has_text text="ELGSSDLTAR" />
+                    <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t13\t1\t995\t0.002\d+\t1\t0\tYes\t10.3\d+\t8.23\d+"/>
+                    <has_n_columns n="22" />
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 **PepQuery2**