--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LowMemPeakPickerHiResRandomAccess.xml	Mon Feb 12 13:12:32 2018 -0500
@@ -0,0 +1,137 @@
+<?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 CTDConverter.-->
+<!--Proposed Tool Section: [Utilities]-->
+<tool id="LowMemPeakPickerHiRes_RandomAccess" name="LowMemPeakPickerHiResRandomAccess" version="2.3.0">
+  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <macros>
+    <token name="@EXECUTABLE@">LowMemPeakPickerHiResRandomAccess</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>LowMemPeakPickerHiResRandomAccess
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_algorithm_signal_to_noise:
+  -algorithm:signal_to_noise $param_algorithm_signal_to_noise
+#end if
+
+#if $rep_param_algorithm_ms_levels:
+-algorithm:ms_levels
+  #for token in $rep_param_algorithm_ms_levels:
+    #if " " in str(token):
+      "$token.param_algorithm_ms_levels"
+    #else
+      $token.param_algorithm_ms_levels
+    #end if
+  #end for
+#end if
+#if $param_algorithm_report_FWHM:
+  -algorithm:report_FWHM
+#end if
+#if $param_algorithm_report_FWHM_unit:
+  -algorithm:report_FWHM_unit
+  #if " " in str($param_algorithm_report_FWHM_unit):
+    "$param_algorithm_report_FWHM_unit"
+  #else
+    $param_algorithm_report_FWHM_unit
+  #end if
+#end if
+#if $param_algorithm_SignalToNoise_win_len:
+  -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
+#end if
+#if $param_algorithm_SignalToNoise_bin_count:
+  -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
+#end if
+#if $param_algorithm_SignalToNoise_min_required_elements:
+  -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
+#end if
+#if $param_algorithm_SignalToNoise_write_log_messages:
+  -algorithm:SignalToNoise:write_log_messages
+  #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
+    "$param_algorithm_SignalToNoise_write_log_messages"
+  #else
+    $param_algorithm_SignalToNoise_write_log_messages
+  #end if
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_spacing_difference_gap:
+  -algorithm:spacing_difference_gap $adv_opts.param_algorithm_spacing_difference_gap
+#end if
+    #if $adv_opts.param_algorithm_spacing_difference:
+  -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
+#end if
+    #if $adv_opts.param_algorithm_missing:
+  -algorithm:missing $adv_opts.param_algorithm_missing
+#end if
+    #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
+  -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
+#end if
+    #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
+  -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
+#end if
+    #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
+  -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
+#end if
+    #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
+  -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
+#end if
+    #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
+  -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
+    <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
+    <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
+      <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/>
+    <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
+      <option value="relative" selected="true">relative</option>
+      <option value="absolute">absolute</option>
+    </param>
+    <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
+    <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
+    <param name="param_algorithm_SignalToNoise_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) "/>
+    <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <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_spacing_difference_gap" type="float" min="0.0" optional="True" value="4.0" label="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'" help="(-spacing_difference_gap) 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms"/>
+      <param name="param_algorithm_spacing_difference" type="float" min="0.0" optional="True" value="1.5" label="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points" help="(-spacing_difference) If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms"/>
+      <param name="param_algorithm_missing" type="integer" min="0" optional="True" value="1" label="Maximum number of missing points allowed when extending a peak to the left or to the right" help="(-missing) A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms"/>
+      <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) 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"/>
+      <param name="param_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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_algorithm_SignalToNoise_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" format="mzml"/>
+  </outputs>
+  <help>Finds mass spectrometric peaks in profile mass spectra.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiResRandomAccess.html</help>
+</tool>