--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jul 12 08:42:58 2018 -0400
@@ -0,0 +1,215 @@
+<macros>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Job Failed" />
+            <regex match="java.*Exception" level="fatal" description="Java Exception"/>
+            <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
+            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
+        </stdio>
+    </xml>
+    <token name="@ENZYMESCLI@"><![CDATA[
+              #if len($protein_digest_options.digestion.user_enzymes) > 0:
+                  #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
+                     (searchgui com.compomics.cli.enzymes.EnzymesCLI  -out enzymes.json -in enzymes.json
+                     -name $user_enzyme.enzyme_name
+                     #if $user_enzyme.cleave_before:
+                         -cleave_before $user_enzyme.cleave_before
+                     #end if 
+                     #if $user_enzyme.cleave_after:
+                         -cleave_after $user_enzyme.cleave_after
+                     #end if 
+                     #if $user_enzyme.restriction_before:
+                         -restriction_before $user_enzyme.restriction_before
+                     #end if 
+                     #if $user_enzyme.restriction_after:
+                         -restriction_after $user_enzyme.restriction_after
+                     #end if 
+                     ) &&
+                  #end for
+              #end if
+    ]]></token>
+    <token name="@ENZYME_CONFIGUTRATION@">
+            #if len($protein_digest_options.digestion.user_enzymes) > 0:
+              -enzyme_configuration enzymes.json
+            #end if
+    </token>
+    <token name="@GENERAL_PARAMETERS@">
+            -frag_tol '${precursor_options.fragment_tol}'
+            -frag_ppm '${precursor_options.fragment_tol_units}'
+            -prec_tol '${precursor_options.precursor_ion_tol}'
+            -prec_ppm '${precursor_options.precursor_ion_tol_units}'
+
+            -min_charge $precursor_options.min_charge
+            -max_charge $precursor_options.max_charge
+            -fi $precursor_options.forward_ion
+            -ri $precursor_options.reverse_ion
+            -min_isotope ${precursor_options.min_isotope}
+            -max_isotope ${precursor_options.max_isotope}
+            #if $protein_digest_options.digestion.cleavage == 'default':
+              ## -enzyme "Trysin"
+              -mc $protein_digest_options.digestion.missed_cleavages
+            #elif $protein_digest_options.digestion.cleavage == '0':
+              #set $enzymes = []
+              #set $missed_cleavages = []
+              ## #set $specificities = []
+              #if len($protein_digest_options.digestion.digests) > 0:
+                  #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
+                      #silent $enzymes.append(str($digest.enzyme))
+                      #silent $missed_cleavages.append(str($digest.missed_cleavages))
+                      ## #silent $specificities.append(str($digest.specificity))
+                  #end for
+              #end if
+              #if len($protein_digest_options.digestion.user_enzymes) > 0:
+                  #for $i, $user_enzyme in enumerate($protein_digest_options.digestion.user_enzymes):
+                      #silent $enzymes.append(str($user_enzyme.enzyme_name))
+                      #silent $missed_cleavages.append(str($user_enzyme.missed_cleavages))
+                  #end for
+              #end if
+              #if len($enzymes) > 0:
+                -enzyme "#echo ','.join($enzymes)#"
+                -mc "#echo ','.join($missed_cleavages)#"
+                ## -specificity "#echo ','.join($specificities)#"
+              #end if
+            #else:
+               -digestion $protein_digest_options.digestion.cleavage
+            #end if
+
+            #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
+            #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
+            #if $fixed_mods_str
+                -fixed_mods "$fixed_mods_str"
+            #end if
+            #if $variable_mods_str
+                -variable_mods "$variable_mods_str"
+            #end if
+
+    </token>
+    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
+    <token name="@SEARCHGUI_VERSION@">3.3.3</token>
+    <xml name="general_options">
+
+        <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
+            <conditional name="digestion">
+                <param name="cleavage" type="select" label="Digestion">
+                    <option value="default" selected="true">Trypsin</option>
+                    <option value="0">Select Enzymes</option>
+                    <option value="1">Unspecific Cleavage</option>
+                    <option value="2">Whole Protein</option>
+                </param>
+                <when value="default">
+                    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
+                        help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
+                </when>
+                <when value="0">
+                    <repeat name="digests" min="1" title="Enzymes">
+                        <param name="enzyme" type="select" label="Enzyme"
+                            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
+                            <option value="Trypsin">Trypsin</option>
+                            <option value="Arg-C">Arg-C</option>
+                            <option value="CNBr">CNBr</option>
+                            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
+                            <option value="Formic Acid">Formic Acid</option>
+                            <option value="Lys-C">Lys-C</option>
+                            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
+                            <option value="Pepsin A">Pepsin A</option>
+                            <option value="Trypsin + CNBr">Trypsin + CNBr</option>
+                            <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
+                            <option value="Trypsin, no P rule">Trypsin, no P rule</option>
+                            <option value="Whole Protein">Whole Protein</option>
+                            <option value="Asp-N">Asp-N</option>
+                            <option value="Glu-C">Glu-C</option>
+                            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
+                            <option value="Top-Down">Top-Down</option>
+                            <option value="Semi-Tryptic">Semi-Tryptic</option>
+                            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
+                            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
+                            <option value="Asp-N (DE)">Asp-N (DE)</option>
+                            <option value="Glu-C (DE)">Glu-C (DE)</option>
+                            <option value="Lys-N (K)">Lys-N (K)</option>
+                            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
+                            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
+                            <option value="Semi-Glu-C">Semi-Glu-C</option>
+                            <option value="LysargiNase">LysargiNase</option>
+                            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
+                            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
+                            <option value="Semi-Arg-C">Semi-Arg-C</option>
+                            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
+                            <option value="Arg-N">Arg-N</option>
+                            <option value="Semi-Arg-N">Semi-Arg-N</option>
+                        </param>
+                        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
+                            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
+                        <!--
+                        <param name="specificity" type="select" label="Specificity">
+                            <option value="0" selected="true">Specific at both termini</option>
+                            <option value="1">Semi-Specific - one terminus</option>
+                            <option value="2">Specific at the N-terminus only</option>
+                            <option value="3">Specific at the C-terminus only</option>
+                        </param>
+                        -->
+                    </repeat>
+                </when>
+                <when value="1"/>
+                <when value="2"/>
+            </conditional>
+        </section>
+
+        <section name="precursor_options" expanded="false" title="Precursor Options">
+            <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
+                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
+                <option value="1">Parts per million (ppm)</option>
+                <option value="0">Daltons</option>
+            </param>
+            <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
+                help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
+            <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
+                help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
+                <option value="1">Parts per million (ppm)</option>
+                <option value="0" selected="true">Daltons</option>
+            </param>
+            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
+                help="Provide error value for fragment ions, based on instrument used"/>
+            <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
+            <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
+            <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
+                <option value="a">a</option>
+                <option value="b" selected="true">b</option>
+                <option value="c">c</option>
+            </param>
+            <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
+                <option value="x">x</option>
+                <option value="y" selected="true">y</option>
+                <option value="z">z</option>
+            </param>
+            <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
+            <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
+        </section>
+
+        <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
+            <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>
+            <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>
+        </section>
+
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/1471-2105-12-70</citation>
+            <citation type="doi">10.1002/pmic.201000595</citation>
+            <citation type="doi">doi:10.1038/nbt.3109</citation>
+        </citations>
+    </xml>
+
+</macros>