--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Sep 20 09:16:44 2019 -0400
@@ -0,0 +1,414 @@
+<macros>
+    <token name="@VERSION@">0.9.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">encyclopedia</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+    <token name="@CMD_IMPORTS@">
+    #import re
+    #set $i_name = None
+    #set $f_name = None
+    #set $l_name = None
+    #set $t_name = None
+    </token>
+
+    <xml name="scan_input">
+        <param argument="-i" type="data" format="mzml" label="Spectrum file, .mzml or .dia"/> 
+    </xml>
+    <token name="@LINK_SCAN_INPUT@"><![CDATA[
+    #set $i_name = $i.display_name
+    ln -s '$i' '$i_name' &&
+    ]]></token>
+    <token name="@SCAN_INPUT@">
+    -i '$i_name'
+    </token>
+
+    <xml name="scan_inputs">
+        <param argument="-i" type="data" format="mzml" multiple="true" label="Spectrum file, .mzml or .dia"/> 
+    </xml>
+    <token name="@LINK_SCAN_INPUTS@"><![CDATA[
+    #set $inputs_dir = 'inputs'
+    mkdir -p $inputs_dir &&
+    #for $sf in $i
+      #set $i_name = $sf.display_name
+      ln -s '$sf' '${inputs_dir}/${i_name}' &&
+    #end for
+    ]]></token>
+    <token name="@SCAN_INPUTS@">
+    -i '$inputs_dir'
+    </token>
+
+    <xml name="fasta_input">
+        <param argument="-f" type="data" format="fasta" label="Background protein fasta database"/> 
+    </xml>
+    <token name="@LINK_FASTA_INPUT@"><![CDATA[
+    #set $f_name = $f.display_name
+    ln -s '$f' '$f_name' &&
+    ]]></token>
+    <token name="@FASTA_INPUT@">
+    -f '$f_name'
+    </token>
+
+    <xml name="target_fasta">
+        <param argument="-t" type="data" format="fasta" label="target FASTA file" optional="true"/> 
+        <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/>
+    </xml>
+    <token name="@LINK_TARGET_FASTA@"><![CDATA[
+    #if $t
+    #set $t_name = $t.display_name
+    ln -s '$t' '$t_name' &&
+    #else
+    #set $t_name = None
+    #end if
+    ]]></token>
+    <token name="@TARGET_FASTA@">
+    #if $t_name
+    -t '$t_name'
+    -tp $tp
+    #end if
+    </token>
+
+    <xml name="lib_input">
+        <param argument="-l" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/> 
+    </xml>
+    <token name="@LINK_LIB_INPUT@"><![CDATA[
+    #set $l_name = $l.display_name
+    cp '$l' $l_name &&
+    ]]></token>
+    <token name="@LIB_INPUT@">
+    -l '$l_name'
+    </token>
+
+    <xml name="common_options">
+        <section name="acquisition" expanded="true" title="Acquisition Options">
+        <param argument="-numberOfExtraDecoyLibrariesSearched" type="float" value="0.0" min="0.0" max="1.0" label="numberOfExtraDecoyLibrariesSearched"/>
+        <param argument="-acquisition" type="select" label="Data Acquization Type">
+            <option value="Non-Overlapping DIA">Non-Overlapping DIA</option>
+            <option value="Overlapping DIA">Overlapping DIA</option>
+        </param>
+        <param argument="-enzyme" type="select" label="Digestion Enzyme">
+             <option value="Trypsin">Trypsin</option>
+             <option value="Trypsin/p">Trypsin/p</option>
+             <option value="Lys-C">Lys-C</option>
+             <option value="Lys-N">Lys-N</option>
+             <option value="Arg-C">Arg-C</option>
+             <option value="Glu-C">Glu-C</option>
+             <option value="Chymotrypsin">Chymotrypsin</option>
+             <option value="Pepsin A">Pepsin A</option>
+             <option value="Elastase">Elastase</option>
+             <option value="Thermolysin">Thermolysin</option>
+             <option value="No Enzyme">No Enzyme</option>
+        </param>
+        <param argument="-frag" type="select" label="Fragmentation">
+            <option value="CID">CID/HCD (B/Y)</option>
+            <option value="HCD">HCD (Y-Only)</option>
+            <option value="ETD">ETD (C/Z/Z+1)</option>
+        </param>
+        </section>
+    </xml>
+    <token name="@COMMON_OPTIONS@">
+    -numberOfExtraDecoyLibrariesSearched $acquisition.numberOfExtraDecoyLibrariesSearched
+    -acquisition '$acquisition.acquisition'
+    -enzyme '$acquisition.enzyme'
+    -frag '$acquisition.frag'
+    </token>
+
+    <xml name="mass_tolerance">
+        <section name="tolerance" expanded="true" title="Tolerance Options">
+        <conditional name="precursor_tolerance">
+            <param argument="-ptolunits" type="select" label="Precursor Mass Tolerance">
+                <option value="PPM">PPM</option>
+                <option value="AMU">AMU</option>
+                <option value="Resolution">Resolution</option>
+            </param>
+            <when value="PPM">
+                <param argument="-ptol" type="float" value="10" min="1.0" max="200.0" label="Precursor Mass Tolerance (PPM)"/>
+            </when>
+            <when value="AMU">
+                <param argument="-ptol" type="float" value=".4" min="1.0" max="1.0" label="Precursor Mass Tolerance (AMU)"/>
+            </when>
+            <when value="Resolution">
+                <param argument="-ptol" type="integer" value="15000" min="5000" max="300000" label="Precursor Mass Tolerance (Resolution)"/>
+            </when>
+        </conditional>
+        <conditional name="fragment_tolerance">
+            <param argument="-ftolunits" type="select" label="Fragment Mass Tolerance">
+                <option value="PPM">PPM</option>
+                <option value="AMU">AMU</option>
+                <option value="Resolution">Resolution</option>
+            </param>
+            <when value="PPM">
+                <param argument="-ftol" type="float" value="10" min="1.0" max="200.0" label="Fragment Mass Tolerance (PPM)"/>
+            </when>
+            <when value="AMU">
+                <param argument="-ftol" type="float" value=".4" min="1.0" max="1.0" label="Fragment Mass Tolerance (AMU)"/>
+            </when>
+            <when value="Resolution">
+                <param argument="-ftol" type="integer" value="15000" min="5000" max="300000" label="Fragment Mass Tolerance (Resolution)"/>
+            </when>
+        </conditional>
+        <yield/>
+        </section>
+    </xml>
+    <token name="@MASS_TOLERANCE@">
+    -ptolunits $tolerance.precursor_tolerance.ptolunits
+    -ptol $tolerance.precursor_tolerance.ptol
+    -ftolunits $tolerance.fragment_tolerance.ftolunits
+    -ftol $tolerance.fragment_tolerance.ftol
+    </token>
+
+    <xml name="mass_library_tolerance">
+        <expand macro="mass_tolerance">
+        <conditional name="library_tolerance">
+            <param argument="-ltolunits" type="select" label="Library Mass Tolerance">
+                <option value="PPM">PPM</option>
+                <option value="AMU">AMU</option>
+                <option value="Resolution">Resolution</option>
+            </param>
+            <when value="PPM">
+                <param argument="-ltol" type="float" value="10" min="1.0" max="200.0" label="Library Mass Tolerance (PPM)"/>
+            </when>
+            <when value="AMU">
+                <param argument="-ltol" type="float" value=".4" min="1.0" max="1.0" label="Library Mass Tolerance (AMU)"/>
+            </when>
+            <when value="Resolution">
+                <param argument="-ltol" type="integer" value="15000" min="5000" max="300000" label="Library Mass Tolerance (Resolution)"/>
+            </when>
+        </conditional>
+        </expand>
+    </xml>
+    <token name="@MASS_LIBRARY_TOLERANCE@">
+    @MASS_TOLERANCE@
+    -ltolunits $tolerance.library_tolerance.ltolunits
+    -ltol $tolerance.library_tolerance.ltol
+    </token>
+
+    <xml name="percolator_options">
+        <section name="percolator" expanded="false" title="Pecolator Options">
+            <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
+            <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
+            <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
+        </section>
+    </xml>
+    <token name="@PERCOLATOR_OPTIONS@">
+    #if str($percolator.percolatorVersionNumber)
+        -percolatorVersionNumber $percolator.percolatorVersionNumber
+    #end if
+    #if str($percolator.percolatorProteinThreshold)
+        -percolatorProteinThreshold $percolator.percolatorProteinThreshold
+    #end if
+    #if str($percolator.percolatorThreshold)
+        -percolatorThreshold $percolator.percolatorThreshold
+    #end if
+    </token>
+
+    <xml name="peak_options">
+        <section name="peak" expanded="false" title="Peak Options">
+            <param argument="-numberOfQuantitativePeaks" type="integer" value="5" min="1" max="100" label="Number of Quantitative Peaks"/>
+            <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Peaks"/>
+            <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="0" max="100" label="Minimum Number of Quantitative Ions"/>
+            <param argument="-minIntensity" type="float" value="-1.0" label="minIntensity"/>
+            <param argument="-expectedPeakWidth" type="float" value="25.0" min="1" max="100.0" label="Expected Peak Width"/>
+            <param argument="-filterPeaklists" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Filter Peak Lists"/>
+        </section>
+    </xml>
+    <token name="@PEAK_OPTIONS@">
+    #if str($peak.numberOfQuantitativePeaks)
+        -numberOfQuantitativePeaks $peak.numberOfQuantitativePeaks
+    #end if
+    #if str($peak.minNumOfQuantitativePeaks)
+        -minNumOfQuantitativePeaks $peak.minNumOfQuantitativePeaks
+    #end if
+    #if str($peak.minQuantitativeIonNumber)
+        -minQuantitativeIonNumber $peak.minQuantitativeIonNumber
+    #end if
+    #if str($peak.minIntensity)
+        -minIntensity $peak.minIntensity
+    #end if
+    #if str($peak.expectedPeakWidth)
+        -expectedPeakWidth $peak.expectedPeakWidth
+    #end if
+    -filterPeaklists $peak.filterPeaklists
+    </token>
+
+    <xml name="window_options">
+        <section name="window" expanded="false" title="Window Options">
+        <param argument="-foffset" type="integer" value="0" label="fragmentOffsetPPM"/>
+        <param argument="-poffset" type="integer" value="0" label="Precursor Offset PPM" help="-poffset"/>
+        <param argument="-precursorIsolationMargin" type="integer" value="0" label="precursorIsolationMargin"/>
+        <param argument="-precursorWindowSize" type="integer" value="-1" label="precursorWindowSize"/>
+        <param argument="-rtWindowInMin" type="float" value="-1.0" label="rtWindowInMin"/>
+        <param argument="-scoringBreadthType" type="select" label="scoringBreadthType">
+            <option value="window">Across entire window</option>
+            <option value="recal20">Recalibrated (20% gradient)</option>
+            <option value="recal">Recalibrated (peak width only)</option>
+            <option value="uncal20">Uncalibrated (20% gradient)</option>
+            <option value="uncal">Uncalibrated (peak width only)</option>
+        </param>
+        </section>
+    </xml>
+    <token name="@WINDOW_OPTIONS@">
+        -foffset $window.foffset
+        -poffset $window.poffset
+        -precursorIsolationMargin $window.precursorIsolationMargin
+        -precursorWindowSize $window.precursorWindowSize
+        -rtWindowInMin $window.rtWindowInMin
+        -scoringBreadthType $window.scoringBreadthType
+    </token>
+
+    <xml name="modification_options">
+        <section name="modifications" expanded="false" title="Modification Options">
+        <param argument="-fixed" type="select" label="Fixed Modification">
+            <option value="C=57.0214635">C=57.0214635</option>
+        </param>
+        <!--
+        <param argument="-localizationModification" type="select" optional="true" label="localizationModification">
+        </param>
+        -->
+        <param argument="-verifyModificationIons" type="boolean" truevalue="true" falsevalue="false" checked="true" label="verifyModificationIons"/>
+        </section>
+    </xml>
+    <token name="@MODIFICATION_OPTIONS@">
+        -verifyModificationIons $modifications.verifyModificationIons
+    </token>
+
+    <xml name="search_options">
+        <section name="search" expanded="false" title="Search Options">
+        <param argument="-minCharge" type="integer" value="2" min="1" max="10" label="minCharge" optional="true"/>
+        <param argument="-maxCharge" type="integer" value="3" min="1" max="10" label="maxCharge" optional="true"/>
+        <param argument="-minLength" type="integer" value="5" min="1" max="100" label="minLength" optional="true"/>
+        <param argument="-maxLength" type="integer" value="100" min="10" max="200" label="maxLength" optional="true"/>
+        <param argument="-minEluteTime" type="integer" value="12" min="1" max="69" label="minEluteTime" optional="true"/>
+        <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="5" label="maxMissedCleavage" optional="true"/>
+        <param argument="-minQuantitativeIonNumber" type="integer" value="3" min="1" max="10" label="minQuantitativeIonNumber" optional="true"/>
+        <param argument="-minNumOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="minNumOfQuantitativePeaks" optional="true"/>
+        <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>
+        <param argument="-alpha" type="float" value="1.8" min="0.0" max="5.0" label="alpha"/>
+        <param argument="-beta" type="float" value="0.4" min="0.0" max="5.0" label="beta"/>
+        <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>
+        <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>
+        </section>
+    </xml>
+    <token name="@SEARCH_OPTIONS@">
+        -minCharge $search.minCharge
+        -maxCharge $search.maxCharge
+        -minLength $search.minLength
+        -maxLength $search.maxLength
+        -minEluteTime $search.minEluteTime
+        -maxMissedCleavage $search.maxMissedCleavage
+        -minQuantitativeIonNumber $search.minQuantitativeIonNumber
+        -minNumOfQuantitativePeaks $search.minNumOfQuantitativePeaks
+        -numberOfQuantitativePeaks $search.numberOfQuantitativePeaks
+        -alpha $search.alpha
+        -beta $search.beta
+        -addDecoysToBackground $search.addDecoysToBackground
+        -dontRunDecoys $search.dontRunDecoys
+    </token>
+minNumOfQuantitativePeaks minQuantitativeIonNumber numberOfQuantitativePeaks numberOfReportedPeaksu
+    <!--
+	+acquisition                (default: overlapping dia)
+	+addDecoysToBackground      (default: false)
+	+alpha                      (default: 1.8)
+	+beta                       (default: 0.4)
+	+dontRunDecoys              (default: false)
+	+enzyme                     (default: trypsin)
+	+filterPeaklists            (default: false)
+	+fixed                      (default: C=57.0214635)
+	+foffset                    (default: 0)
+	=frag                       (default: YONLY)
+	+ftol                       (default: 10)
+	+ftolunits                  (default: ppm)
+	+maxCharge                  (default: 3)
+	+maxLength                  (default: 100)
+	+maxMissedCleavage          (default: 1)
+	+minCharge                  (default: 2)
+	+minEluteTime               (default: 12)
+	+minIntensity               (default: -1.0)
+	+minLength                  (default: 5)
+	+minNumOfQuantitativePeaks  (default: 3)
+	+minQuantitativeIonNumber   (default: 3)
+	+numberOfQuantitativePeaks  (default: 5)
+	-numberOfReportedPeaks      (default: 1)
+	-numberOfThreadsUsed        (default: 12)
+	+percolatorProteinThreshol  (default: 0.01)
+	+percolatorThreshold        (default: 0.01)
+	+percolatorVersionNumber    (default: 3)
+	+poffset                    (default: 0)
+	+precursorIsolationMargin   (default: 0)
+	+precursorWindowSize        (default: -1)
+	+ptol                       (default: 10)
+	+ptolunits                  (default: ppm)
+	-requireVariableMods        (default: false)
+	-variable                   (default: -)
+   --> 
+    <xml name="libexport">
+        <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="true" label="align between files"/>
+    </xml>
+</macros>
+<!--
+e w t x l	param
++:+:+:+:+	i
++:+:+:+:+	l
++:+:+:+:+	f
+
++:+:+:+:+	t
+-:+:-:+:-	tp
+-:+:-:+:+	a
+
++:+:+:+:+	o
+
++:+:+:+:-	acquisition
+-:+:-:+:-	addDecoysToBackground
+-:+:-:+:-	alpha
+-:+:-:+:-	beta
+-:-:-:-:+	blib
+-:+:-:+:-	dontRunDecoys
++:+:+:+:-	enzyme
++:-:+:-:-	expectedPeakWidth
++:+:+:+:-	filterPeaklists
++:+:+:+:+	fixed
++:+:+:+:+	foffset
++:+:+:+:-	frag
++:+:+:+:+	ftol
++:+:+:+:+	ftolunits
++:-:+:-:-	lftol
++:-:+:-:-	lftolunits
++:-:-:-:-	libexport
++:-:+:-:+	localizationModification
+-:+:-:+:-	maxCharge
+-:+:-:+:-	maxLength
+-:+:-:+:-	maxMissedCleavage
+-:+:-:+:-	minCharge
+-:+:-:+:-	minEluteTime
++:+:+:+:-	minIntensity
+-:+:-:+:-	minLength
++:+:+:+:+	minNumOfQuantitativePeaks
++:+:+:+:+	minQuantitativeIonNumber
++:-:+:-:+	numberOfExtraDecoyLibrariesSearched
++:+:+:+:+	numberOfQuantitativePeaks
+-:+:-:+:-	numberOfReportedPeaks
+-:+:-:+:-	numberOfThreadsUsed
+-:-:-:-:+	percolatorLocation
+-:+:-:+:-	percolatorProteinThreshol
++:-:+:-:+	percolatorProteinThreshold
++:+:+:+:+	percolatorThreshold
++:+:+:+:-	percolatorVersionNumber
+-:-:-:-:+	phospho
++:+:+:+:-	poffset
++:+:+:+:-	precursorIsolationMargin
++:+:+:+:-	precursorWindowSize
++:+:+:+:-	ptol
++:+:+:+:-	ptolunits
+-:+:-:+:-	requireVariableMods
++:-:+:-:-	rtWindowInMin
++:-:+:-:-	scoringBreadthType
+-:+:-:+:-	variable
++:-:+:-:-	verifyModificationIons
+-->