--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ERPairFinder.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,73 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="ERPairFinder" name="ERPairFinder" version="2.0.0">
+  <description>Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ERPairFinder</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ERPairFinder
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_pair_in:
+  -pair_in $param_pair_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_feature_out:
+  -feature_out $param_feature_out
+#end if
+#if $param_precursor_mass_tolerance:
+  -precursor_mass_tolerance $param_precursor_mass_tolerance
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_RT_tolerance:
+  -RT_tolerance $adv_opts.param_RT_tolerance
+#end if
+    #if $adv_opts.param_max_charge:
+  -max_charge $adv_opts.param_max_charge
+#end if
+    #if $adv_opts.param_intensity_threshold:
+  -intensity_threshold $adv_opts.param_intensity_threshold
+#end if
+    #if $adv_opts.param_max_isotope:
+  -max_isotope $adv_opts.param_max_isotope
+#end if
+    #if $adv_opts.param_expansion_range:
+  -expansion_range $adv_opts.param_expansion_range
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the ER spectra" help="(-in) "/>
+    <param name="param_pair_in" type="data" format="txt" optional="False" label="Pair-file in the format: m/z-light m/z-heavy charge rt" help="(-pair_in) "/>
+    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="0.3" label="Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features" help="(-precursor_mass_tolerance) "/>
+    <expand macro="advanced_options">
+      <param name="param_RT_tolerance" type="float" min="1.0" optional="True" value="200.0" label="Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file" help="(-RT_tolerance) "/>
+      <param name="param_max_charge" type="integer" min="1" optional="True" value="3" label="Maximal charge state features should be search fo" help="(-max_charge) "/>
+      <param name="param_intensity_threshold" type="float" min="-1.0" optional="True" value="-1.0" label="Intensity threshold, for the meaning see the documentation of the IsotopeWaveletFeatureFinder documentation" help="(-intensity_threshold) "/>
+      <param name="param_max_isotope" type="integer" min="2" optional="True" value="3" label="Max isotope of the isotope distribution to be considered" help="(-max_isotope) "/>
+      <param name="param_expansion_range" type="float" min="0.0" optional="True" value="5.0" label="The range that is used to extend the isotope distribution with null intensity peaks in Th" help="(-expansion_range) "/>
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="consensusxml"/>
+    <data name="param_feature_out" format="featurexml"/>
+  </outputs>
+  <help>**What it does**
+
+Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_ERPairFinder.html</help>
+  <expand macro="references"/>
+</tool>