# HG changeset patch
# User galaxyp
# Date 1494422578 14400
# Node ID 49f8c1b0542547d8a9257247a4f1971d2a41558d
# Parent  84dcffe178959567a2779c7b3e7443765a78a1bc
Uploaded

diff -r 84dcffe17895 -r 49f8c1b05425 peptide_shaker.xml
--- a/peptide_shaker.xml	Fri Apr 21 15:14:41 2017 -0400
+++ b/peptide_shaker.xml	Wed May 10 09:22:58 2017 -0400
@@ -51,8 +51,9 @@
                         -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
                     #end if
                 #end if
+                -ptm_alignment "${processing_options.ptm_alignment}"
+                -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
                 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
-                -ptm_alignment "${processing_options.ptm_alignment}"
             #end if
 
            ##Optional filtering parameters:
@@ -205,6 +206,7 @@
                     <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
                         <option value="0" selected="True">A-score</option>
                         <option value="1">PhosphoRS</option>
+                        <option value="2">None</option>
                     </param>
                     <when value="0" />
                     <when value="1">
@@ -212,7 +214,13 @@
                         <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
                             help="Automatic mode will be used if not set" />
                     </when>
+                    <when value="2" />
                 </conditional>
+                <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
+                     <option value="0">Character Sequence</option>
+                     <option value="1" selected="true">Amino Acids</option>
+                     <option value="2">Indistinguishable Amino Acids</option>
+                </param>
                 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
                 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
             </when>