--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PeakPickerHiRes.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,62 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PeakPickerHiRes" name="PeakPickerHiRes" version="1.12.0">
+  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PeakPickerHiRes</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PeakPickerHiRes
+
+-in ${param_in}
+-out ${param_out}
+-processOption inmemory
+-threads \${GALAXY_SLOTS:-24} 
+-algorithm:signal_to_noise ${param_signal_to_noise}
+-algorithm:ms_levels ${param_ms_levels}
+-algorithm:SignalToNoise:win_len ${param_win_len}
+-algorithm:SignalToNoise:bin_count ${param_bin_count}
+-algorithm:SignalToNoise:min_required_elements ${param_min_required_elements}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -algorithm:spacing_difference_gap ${adv_opts.param_spacing_difference_gap}
+    -algorithm:spacing_difference ${adv_opts.param_spacing_difference}
+    -algorithm:missing ${adv_opts.param_missing}
+    -algorithm:SignalToNoise:max_intensity ${adv_opts.param_max_intensity}
+    -algorithm:SignalToNoise:auto_max_stdev_factor ${adv_opts.param_auto_max_stdev_factor}
+    -algorithm:SignalToNoise:auto_max_percentile ${adv_opts.param_auto_max_percentile}
+    -algorithm:SignalToNoise:auto_mode ${adv_opts.param_auto_mode}
+    -algorithm:SignalToNoise:noise_for_empty_window ${adv_opts.param_noise_for_empty_window}
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/>
+    <param name="param_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise)"/>
+    <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1 2" label="List of MS levels for which the peak picking is applied. Other scans are copied to the output without changes." help="(-ms_levels)"/>
+    <param name="param_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len)"/>
+    <param name="param_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count)"/>
+    <param name="param_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements)"/>
+    <expand macro="advanced_options">
+      <param name="param_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="Maximum allowed m/z distance between data points in multiples of the minimal difference, above which a data point no longer belongs to the peak." help="(-spacing_difference_gap)"/>
+      <param name="param_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed distance between peaks in multiples of the minimal difference. A higher value is implies a less stringent peak definition since individual signals within the peaks are allowed to further apart. E.g. if the value is set to 1.5 and in a peak the minimal spacing between peaks is 10 mDa, then only signals at most 15 mDa apart will be added to the peak." help="(-spacing_difference)"/>
+      <param name="param_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points." help="(-missing)"/>
+      <param name="param_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well.  If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." help="(-max_intensity)"/>
+      <param name="param_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor)"/>
+      <param name="param_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile)"/>
+      <param name="param_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode)"/>
+      <param name="param_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output peak file " format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerHiRes.html
+
+@REFERENCES@
+</help>
+</tool>