--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMultiplex.xml	Wed Mar 01 12:37:44 2017 -0500
@@ -0,0 +1,188 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Quantitation]-->
+<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0">
+  <description>Determination of peak ratios in LC-MS data</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureFinderMultiplex
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_features:
+  -out_features $param_out_features
+#end if
+#if $param_out_mzq:
+  -out_mzq $param_out_mzq
+#end if
+#if $param_algorithm_labels:
+  -algorithm:labels     "$param_algorithm_labels"
+#end if
+#if $param_algorithm_charge:
+  -algorithm:charge     "$param_algorithm_charge"
+#end if
+#if $param_algorithm_rt_typical:
+  -algorithm:rt_typical $param_algorithm_rt_typical
+#end if
+#if $param_algorithm_rt_min:
+  -algorithm:rt_min $param_algorithm_rt_min
+#end if
+#if $param_algorithm_mz_tolerance:
+  -algorithm:mz_tolerance $param_algorithm_mz_tolerance
+#end if
+#if $param_algorithm_mz_unit:
+  -algorithm:mz_unit $param_algorithm_mz_unit
+#end if
+#if $param_algorithm_intensity_cutoff:
+  -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
+#end if
+#if $param_algorithm_peptide_similarity:
+  -algorithm:peptide_similarity $param_algorithm_peptide_similarity
+#end if
+#if $param_algorithm_averagine_similarity:
+  -algorithm:averagine_similarity $param_algorithm_averagine_similarity
+#end if
+#if $param_algorithm_missed_cleavages:
+  -algorithm:missed_cleavages $param_algorithm_missed_cleavages
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_isotopes_per_peptide:
+  -algorithm:isotopes_per_peptide     "$adv_opts.param_algorithm_isotopes_per_peptide"
+#end if
+    #if $adv_opts.param_algorithm_averagine_similarity_scaling:
+  -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
+#end if
+    #if $adv_opts.param_algorithm_knock_out:
+  -algorithm:knock_out
+#end if
+    #if $adv_opts.param_algorithm_averagine_type:
+  -algorithm:averagine_type $adv_opts.param_algorithm_averagine_type
+#end if
+    #if $adv_opts.param_labels_Arg6:
+  -labels:Arg6 $adv_opts.param_labels_Arg6
+#end if
+    #if $adv_opts.param_labels_Arg10:
+  -labels:Arg10 $adv_opts.param_labels_Arg10
+#end if
+    #if $adv_opts.param_labels_Lys4:
+  -labels:Lys4 $adv_opts.param_labels_Lys4
+#end if
+    #if $adv_opts.param_labels_Lys6:
+  -labels:Lys6 $adv_opts.param_labels_Lys6
+#end if
+    #if $adv_opts.param_labels_Lys8:
+  -labels:Lys8 $adv_opts.param_labels_Lys8
+#end if
+    #if $adv_opts.param_labels_Leu3:
+  -labels:Leu3 $adv_opts.param_labels_Leu3
+#end if
+    #if $adv_opts.param_labels_Dimethyl0:
+  -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
+#end if
+    #if $adv_opts.param_labels_Dimethyl4:
+  -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
+#end if
+    #if $adv_opts.param_labels_Dimethyl6:
+  -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
+#end if
+    #if $adv_opts.param_labels_Dimethyl8:
+  -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
+#end if
+    #if $adv_opts.param_labels_ICPL0:
+  -labels:ICPL0 $adv_opts.param_labels_ICPL0
+#end if
+    #if $adv_opts.param_labels_ICPL4:
+  -labels:ICPL4 $adv_opts.param_labels_ICPL4
+#end if
+    #if $adv_opts.param_labels_ICPL6:
+  -labels:ICPL6 $adv_opts.param_labels_ICPL6
+#end if
+    #if $adv_opts.param_labels_ICPL10:
+  -labels:ICPL10 $adv_opts.param_labels_ICPL10
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="LC-MS dataset in centroid or profile mode" help="(-in) "/>
+    <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10]        ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6]        ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_charge" type="text" size="30" value="1:4" label="Range of charge states in the sample, i.e" help="(-charge) min charge : max charge">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_algorithm_rt_typical" type="float" min="0.0" optional="True" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(-rt_typical) (This is not an upper bound. Peptides that elute for longer will be reported.)"/>
+    <param name="param_algorithm_rt_min" type="float" min="0.0" optional="True" value="2.0" label="Lower bound for the retention time [s]" help="(-rt_min) (Any peptides seen for a shorter time period are not reported.)"/>
+    <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="6.0" label="m/z tolerance for search of peak patterns" help="(-mz_tolerance) "/>
+    <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of the 'mz_tolerance' paramete" help="(-mz_unit) ">
+      <option value="Da">Da</option>
+      <option value="ppm" selected="true">ppm</option>
+    </param>
+    <param name="param_algorithm_intensity_cutoff" type="float" min="0.0" optional="True" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help="(-intensity_cutoff) "/>
+    <param name="param_algorithm_peptide_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="(-peptide_similarity) This parameter is a lower bound on their similarity"/>
+    <param name="param_algorithm_averagine_similarity" type="float" min="-1.0" max="1.0" optional="True" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="(-averagine_similarity) This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
+    <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+      <param name="param_algorithm_isotopes_per_peptide" type="text" size="30" value="3:6" label="Range of isotopes per peptide in the sample" help="(-isotopes_per_peptide) For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
+      <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
+      <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
+        <option value="peptide" selected="true">peptide</option>
+        <option value="RNA">RNA</option>
+        <option value="DNA">DNA</option>
+      </param>
+      <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Arg6) "/>
+      <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help="(-Arg10) "/>
+      <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help="(-Lys4) "/>
+      <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Lys6) "/>
+      <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help="(-Lys8) "/>
+      <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help="(-Leu3) "/>
+      <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help="(-Dimethyl0) "/>
+      <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help="(-Dimethyl4) "/>
+      <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help="(-Dimethyl6) "/>
+      <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help="(-Dimethyl8) "/>
+      <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help="(-ICPL0) "/>
+      <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help="(-ICPL4) "/>
+      <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help="(-ICPL6) "/>
+      <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help="(-ICPL10) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="consensusxml"/>
+    <data name="param_out_features" format="featurexml"/>
+    <data name="param_out_mzq" format="mzq"/>
+  </outputs>
+  <help>Determination of peak ratios in LC-MS data
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMultiplex.html</help>
+</tool>