--- a/ProteinQuantifier.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/ProteinQuantifier.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,67 +1,126 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="ProteinQuantifier" name="ProteinQuantifier" version="1.12.0">
-  <description>Compute peptide and protein abundances</description>
-  <macros>
-    <token name="@EXECUTABLE@">ProteinQuantifier</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>ProteinQuantifier
+<?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="ProteinQuantifier" name="ProteinQuantifier" version="2.0.0">
+    <description>Compute peptide and protein abundances</description>
+    <macros>
+      <token name="@EXECUTABLE@">ProteinQuantifier</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>ProteinQuantifier
 
--in ${param_in}
--protxml ${param_protxml}
--out ${param_out}
--peptide_out ${param_peptide_out}
--mzTab_out ${param_mzTab_out}
--top ${param_top}
--average ${param_average}
-${param_include_all}
-${param_filter_charge}
-${param_ratios}
-${param_ratiosSILAC}
--threads \${GALAXY_SLOTS:-24} 
-${param_normalize}
-${param_fix_peptides}
--format:separator ${param_separator}
--format:quoting ${param_quoting}
--format:replacement ${param_replacement}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_protein_groups:
+  -protein_groups $param_protein_groups
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_peptide_out:
+  -peptide_out $param_peptide_out
+#end if
+#if $param_top:
+  -top $param_top
+#end if
+#if $param_average:
+  -average
+  #if &quot; &quot; in str($param_average):
+    &quot;$param_average&quot;
+  #else
+    $param_average
+  #end if
+#end if
+#if $param_include_all:
+  -include_all
+#end if
+#if $param_filter_charge:
+  -filter_charge
+#end if
+#if $param_ratios:
+  -ratios
+#end if
+#if $param_ratiosSILAC:
+  -ratiosSILAC
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_consensus_normalize:
+  -consensus:normalize
+#end if
+#if $param_consensus_fix_peptides:
+  -consensus:fix_peptides
+#end if
+#if $param_format_separator:
+  -format:separator     &quot;$param_format_separator&quot;
+#end if
+#if $param_format_quoting:
+  -format:quoting
+  #if &quot; &quot; in str($param_format_quoting):
+    &quot;$param_format_quoting&quot;
+  #else
+    $param_format_quoting
+  #end if
+#end if
+#if $param_format_replacement:
+  -format:replacement     &quot;$param_format_replacement&quot;
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" label="Input file" help="(-in)"/>
-    <param name="param_protxml" type="data" format="idXML" optional="True" label="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." help="(-protxml)"/>
-    <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top)"/>
-    <param name="param_average" type="select" optional="True" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average)">
-      <option value="median">median</option>
-      <option value="mean">mean</option>
-      <option value="sum">sum</option>
-    </param>
-    <param name="param_include_all" type="boolean" truevalue="-include_all true" falsevalue="-include_all false" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all)"/>
-    <param name="param_filter_charge" type="boolean" truevalue="-filter_charge true" falsevalue="-filter_charge false" checked="false" optional="True" label="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." help="(-filter_charge)"/>
-    <param name="param_ratios" type="boolean" truevalue="-ratios true" falsevalue="-ratios false" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) ..." help="(-ratios)"/>
-    <param name="param_ratiosSILAC" type="boolean" truevalue="-ratiosSILAC true" falsevalue="-ratiosSILAC false" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)" help="(-ratiosSILAC)"/>
-    <param name="param_normalize" type="boolean" truevalue="-consensus:normalize true" falsevalue="-consensus:normalize false" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize)"/>
-    <param name="param_fix_peptides" type="boolean" truevalue="-consensus:fix_peptides true" falsevalue="-consensus:fix_peptides false" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." help="(-fix_peptides)"/>
-    <param name="param_separator" type="text" size="20" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator)"/>
-    <param name="param_quoting" type="select" optional="True" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
-      <option value="none">none</option>
-      <option value="double">double</option>
-      <option value="escape">escape</option>
-    </param>
-    <param name="param_replacement" type="text" size="20" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file for protein abundances" format="tabular"/>
-    <data name="param_peptide_out" label="Output file for peptide abundances" format="tabular"/>
-    <data name="param_mzTab_out" label="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Compute peptide and protein abundances
+    <inputs>
+      <param format="xml,consensusxml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
+      <param format="xml" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification" label="Protein inference results for the identification runs that were used to annotate the input (" name="param_protein_groups" optional="True" type="data"/>
+      <param help="(-top) " label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" min="0" name="param_top" optional="True" type="integer" value="3"/>
+      <param help="(-average) " label="Averaging method used to compute protein abundances from peptide abundances" name="param_average" optional="True" type="select" value="median">
+        <option value="median">median</option>
+        <option value="mean">mean</option>
+        <option value="weighted_mean">weighted_mean</option>
+        <option value="sum">sum</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-include_all) " label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" name="param_include_all" optional="True" truevalue="-include_all" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states" label="Distinguish between charge states of a peptide" name="param_filter_charge" optional="True" truevalue="-filter_charge" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-ratios) Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) " label="Add the log2 ratios of the abundance values to the output" name="param_ratios" optional="True" truevalue="-ratios" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)" label="Add the log2 ratios for a triple SILAC experiment to the output" name="param_ratiosSILAC" optional="True" truevalue="-ratiosSILAC" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-normalize) " label="Scale peptide abundances so that medians of all samples are equal" name="param_consensus_normalize" optional="True" truevalue="-consensus:normalize" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)" label="Use the same peptides for protein quantification across all samples" name="param_consensus_fix_peptides" optional="True" truevalue="-consensus:fix_peptides" type="boolean"/>
+      <param help="(-separator) " label="Character(s) used to separate fields; by default, the 'tab' character is used" name="param_format_separator" size="30" type="text">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-quoting) " label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" name="param_format_quoting" optional="True" type="select" value="double">
+        <option value="none">none</option>
+        <option value="double">double</option>
+        <option value="escape">escape</option>
+      </param>
+      <param help="(-replacement) " label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" name="param_format_replacement" size="30" type="text" value="_">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="param_out"/>
+      <data format="tabular" name="param_peptide_out"/>
+    </outputs>
+    <help>Compute peptide and protein abundances
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html</help>
+  </tool>