--- a/msgfplus.xml	Fri Nov 06 14:31:57 2015 -0500
+++ b/msgfplus.xml	Wed Nov 11 16:13:39 2015 -0500
@@ -19,11 +19,24 @@
         ln -s '$s' '${input_name}' &&
         ln -s '$d' '${db_name}' &&
 
-        java -jar \$(which MSGFPlus.jar)
+        echo \\#Mods > Mods.txt &&
+        #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
+        #for $mod in $common_mods.split(",")
+          echo '$mod.replace("_", ",")' >> Mods.txt &&
+        #end for
+
+        #for $mod in $custom_mods
+          echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
+        #end for
+
+        msgfjar=\$(which MSGFPlus.jar) &&
+        ( [ -f "\$msgfjar" ] || (echo MSGFPlus.jar not found && exit 1)) &&
+
+        java -jar \$msgfjar
             -s '$input_name'
             -d '$db_name'
             -thread \${GALAXY_SLOTS:-1}
-
+            -mod Mods.txt
             -tda $tda
             -t $t$precursor_ion_tol_units
             -ti $advanced.isotope_low,$advanced.isotope_high
@@ -74,19 +87,89 @@
             <option value="1">Semi-specific (at least one terminus must match cleavage rules)</option>
             <option value="0">Non-specific (neither terminus is required to match cleavage rules)</option>
         </param>
-        <!--
-        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
-            <options from_file="searchgui_mods.loc">
-                <column name="name" index="0" />
-                <column name="value" index="0" />
-            </options>
+
+        <param name="common_fixed_modifications" type="select" label="Common Fixed Modifications" multiple="true" help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
+            <option value="C2H3N1O1_C_fix_any_Carbamidomethyl" selected="true">Carbamidomethyl C</option>
+            <option value="144.102063_*_fix_N-term_iTRAQ4plex">iTRAQ 4-plex N-term</option>
+            <option value="144.102063_K_fix_any_iTRAQ4plex">iTRAQ 4-plex K</option>
+            <option value="225.155833_*_fix_N-term_TMT6plex">TMT 2-plex N-term</option>
+            <option value="225.155833_K_fix_any_TMT6plex">TMT 2-plex K</option>
+            <option value="229.162932_*_fix_N-term_TMT6plex">TMT 6-or-10-plex N-term</option>
+            <option value="229.162932_K_fix_any_TMT6plex">TMT 6-or-10-plex K</option>
+            <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
+        </param>
+        <param name="common_variable_modifications" type="select" label="Common Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
+            <option value="C2H2O1_K_opt_any_Acetyl">Acetylation K</option>
+            <option value="C2H2O_*_opt_Prot-N-term_Acetyl">Acetylation Protein N-term</option>
+            <option value="C2H3NO_C_opt_any_Carbamidomethyl">Carbamidomethyl C</option>
+            <option value="C2H3NO_*_opt_N-term_Carbamidomethyl">Carbamidomethyl N-term</option>
+            <option value="H-1N-1O1_N_opt_any_Deamidated">Deamidation N</option>
+            <option value="H-1N-1O1_Q_opt_any_Deamidated">Deamidation Q</option>
+            <option value="CH2_K_opt_any_Methyl">Methylation K</option>
+            <option value="O1_M_opt_any_Oxidation" selected="true">Oxidation M</option>
+            <option value="HO3P_S_opt_any_Phospho">Phosphorylation S</option>
+            <option value="HO3P_T_opt_any_Phospho">Phosphorylation T</option>
+            <option value="HO3P_Y_opt_any_Phospho">Phosphorylation Y</option>
+            <option value="H-2O-1_E_opt_N-term_Glu-&gt;pyro-Glu">Pyro-glu from E</option>
+            <option value="H-3N-1_Q_opt_N-term_Gln-&gt;pyro-Glu">Pyro-glu from Q</option>
+            <sanitizer invalid_char=""><valid initial="string.printable"><add value="["/><add value="]"/><add value=","/><add value="-"/></valid><mapping initial="none"></mapping></sanitizer>
         </param>
-        <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
-            <options from_file="searchgui_mods.loc">
-                <column name="name" index="0" />
-                <column name="value" index="0" />
-            </options>
-        </param>-->
+        
+        <repeat name="custom_mods" title="Custom Modifications" help="Specify modifications with custom parameters">
+            <param name="formula_or_mass" type="text" label="Formula or Mass">
+                <sanitizer>
+                    <valid initial="string.digits">
+                        <add value="C"/>
+                        <add value="H"/>
+                        <add value="O"/>
+                        <add value="N"/>
+                        <add value="S"/>
+                        <add value="P"/>
+                        <add value="B"/><add value="r"/>
+                        <add value="C"/><add value="l"/>
+                        <add value="F"/><add value="e"/>
+                        <add value="S"/>
+                        <add value="."/>
+                        <add value="-"/>
+                    </valid>
+                </sanitizer>
+            </param>
+            <param name="aa_specificity" type="select" multiple="true" label="Amino Acid Specificity">
+                <option value="*" selected="true">Any</option>
+                <option value="A">A</option>
+                <option value="C">C</option>
+                <option value="D">D</option>
+                <option value="E">E</option>
+                <option value="F">F</option>
+                <option value="G">G</option>
+                <option value="H">H</option>
+                <option value="I">I</option>
+                <option value="K">K</option>
+                <option value="L">L</option>
+                <option value="M">M</option>
+                <option value="N">N</option>
+                <option value="P">P</option>
+                <option value="Q">Q</option>
+                <option value="R">R</option>
+                <option value="S">S</option>
+                <option value="T">T</option>
+                <option value="V">V</option>
+                <option value="W">W</option>
+                <option value="Y">Y</option>
+            </param>
+            <param name="fix_or_opt" type="select" label="Variable or Fixed?">
+                <option value="opt" selected="true">Variable</option>
+                <option value="fix">Fixed</option>
+            </param>
+            <param name="position_specificity" type="select" label="Positional Specificity">
+                <option value="any" selected="true">Any</option>
+                <option value="n-term">Peptide N-terminal</option>
+                <option value="c-term">Peptide C-terminal</option>
+                <option value="prot-n-term">Protein N-terminal</option>
+                <option value="prot-c-term">Protein C-terminal</option>
+            </param>
+            <param name="mod_name" type="text" label="Name" help="If this mod has an entry there in Unimod, this name should match its name there" />
+        </repeat>
 
         <!-- MS-GF+ ADVANCED PARAMETERS -->
         <section name="advanced" title="Advanced Options">
@@ -122,7 +205,13 @@
         <test>
             <param name="s" value="input/201208-378803.mzML" />
             <param name="d" value="input/cow.protein.PRG2012-subset.fasta" />
-            <output name="output" file="201208-378803-msgf.mzid" lines_diff="12" />
+            <param name="tda" value="1" />
+            <param name="ntt" value="1" />
+            <param name="t" value="50" />
+            <param name="precursor_ion_tol_units" value="ppm" />            
+            <param name="common_fixed_modifications" value="" />
+            <param name="common_variable_modifications" value="" />
+            <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
         </test>
         <test>
             <param name="s" value="input/201208-378803.mzML" />
@@ -132,10 +221,9 @@
             <param name="precursor_ion_tol_units" value="Da" />
             <param name="isotope_low" value="-1" />
             <param name="isotope_high" value="0" />
-            <param name="m" value="1" />
-            <param name="inst" value="1" />
+            <param name="m" value="3" />
+            <param name="inst" value="2" />
             <param name="e" value="3" />
-            <param name="ntt" value="1" />
             <param name="protocol" value="2" />
             <param name="minLength" value="10" />
             <param name="maxLength" value="20" />
@@ -143,7 +231,23 @@
             <param name="maxCharge" value="6" />
             <param name="n" value="2" />
             <param name="addFeatures" value="1" />
-            <output name="output" file="201208-378803-msgf-2mmu-semi-tryptic.mzid" lines_diff="12" />
+
+            <param name="common_fixed_modifications" value="C2H3N1O1_C_fix_any_Carbamidomethyl,144.102063_*_fix_N-term_iTRAQ4plex,144.102063_K_fix_any_iTRAQ4plex" />
+            <param name="common_variable_modifications" value="O1_M_opt_any_Oxidation,H-3N-1_Q_opt_N-term_Gln->pyro-Glu" />
+
+            <param name="custom_mods_0|formula_or_mass" value="C-2H-2O-2" />
+            <param name="custom_mods_0|aa_specificity" value="G" />
+            <param name="custom_mods_0|fix_or_opt" value="opt" />
+            <param name="custom_mods_0|position_specificity" value="c-term" />
+            <param name="custom_mods_0|mod_name" value="Gly-loss+Amide" />
+
+            <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
+            <param name="custom_mods_1|aa_specificity" value="CS" />
+            <param name="custom_mods_1|fix_or_opt" value="opt" />
+            <param name="custom_mods_1|position_specificity" value="any" />
+            <param name="custom_mods_1|mod_name" value="cGMP" />
+
+            <output name="output" file="201208-378803-msgf-2mmu-tryptic-many_mods.mzid" lines_diff="6" />
         </test>
     </tests>
     <help>