--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeatureFinderMetabo.xml	Wed Mar 01 12:21:06 2017 -0500
@@ -0,0 +1,171 @@
+<?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="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.1.0">
+  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
+  <macros>
+    <token name="@EXECUTABLE@">FeatureFinderMetabo</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>FeatureFinderMetabo
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_algorithm_common_noise_threshold_int:
+  -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
+#end if
+#if $param_algorithm_common_chrom_peak_snr:
+  -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
+#end if
+#if $param_algorithm_common_chrom_fwhm:
+  -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
+#end if
+#if $param_algorithm_mtd_mass_error_ppm:
+  -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
+#end if
+#if $param_algorithm_mtd_reestimate_mt_sd:
+  -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
+#end if
+#if $param_algorithm_mtd_quant_method:
+  -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
+#end if
+#if $param_algorithm_epd_enabled:
+  -algorithm:epd:enabled $param_algorithm_epd_enabled
+#end if
+#if $param_algorithm_epd_width_filtering:
+  -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
+#end if
+#if $param_algorithm_ffm_charge_lower_bound:
+  -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
+#end if
+#if $param_algorithm_ffm_charge_upper_bound:
+  -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
+#end if
+#if $param_algorithm_ffm_enable_RT_filtering:
+  -algorithm:ffm:enable_RT_filtering $param_algorithm_ffm_enable_RT_filtering
+#end if
+#if $param_algorithm_ffm_isotope_filtering_model:
+  -algorithm:ffm:isotope_filtering_model $param_algorithm_ffm_isotope_filtering_model
+#end if
+#if $param_algorithm_ffm_mz_scoring_13C:
+  -algorithm:ffm:mz_scoring_13C
+#end if
+#if $param_algorithm_ffm_report_convex_hulls:
+  -algorithm:ffm:report_convex_hulls
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
+  -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
+#end if
+    #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
+  -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
+#end if
+    #if $adv_opts.param_algorithm_mtd_min_sample_rate:
+  -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
+#end if
+    #if $adv_opts.param_algorithm_mtd_min_trace_length:
+  -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
+#end if
+    #if $adv_opts.param_algorithm_mtd_max_trace_length:
+  -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
+#end if
+    #if $adv_opts.param_algorithm_epd_min_fwhm:
+  -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
+#end if
+    #if $adv_opts.param_algorithm_epd_max_fwhm:
+  -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
+#end if
+    #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
+  -algorithm:epd:masstrace_snr_filtering
+#end if
+    #if $adv_opts.param_algorithm_ffm_local_rt_range:
+  -algorithm:ffm:local_rt_range $adv_opts.param_algorithm_ffm_local_rt_range
+#end if
+    #if $adv_opts.param_algorithm_ffm_local_mz_range:
+  -algorithm:ffm:local_mz_range $adv_opts.param_algorithm_ffm_local_mz_range
+#end if
+    #if $adv_opts.param_algorithm_ffm_report_summed_ints:
+  -algorithm:ffm:report_summed_ints
+#end if
+    #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
+  -algorithm:ffm:use_smoothed_intensities $adv_opts.param_algorithm_ffm_use_smoothed_intensities
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
+    <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
+    <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
+    <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>
+    <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/>
+    <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) ">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data">
+      <option value="area" selected="true">area</option>
+      <option value="median">median</option>
+    </param>
+    <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="(-enabled) Disable for direct injection">
+      <option value="true" selected="true">true</option>
+      <option value="false">false</option>
+    </param>
+    <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+      <option value="off">off</option>
+      <option value="fixed" selected="true">fixed</option>
+      <option value="auto">auto</option>
+    </param>
+    <param name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help="(-charge_lower_bound) "/>
+    <param name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help="(-charge_upper_bound) "/>
+    <param name="param_algorithm_ffm_enable_RT_filtering" display="radio" type="select" optional="False" value="true" label="Require sufficient overlap in RT while assembling mass traces" help="(-enable_RT_filtering) Disable for direct injection data">
+      <option value="false">false</option>
+      <option value="true" selected="true">true</option>
+    </param>
+    <param name="param_algorithm_ffm_isotope_filtering_model" display="radio" type="select" optional="False" value="metabolites (5% RMS)" label="Remove/score candidate assemblies based on isotope intensities" help="(-isotope_filtering_model) SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
+      <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
+      <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
+      <option value="peptides">peptides</option>
+      <option value="none">none</option>
+    </param>
+    <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
+    <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
+    <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_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <option value="outlier" selected="true">outlier</option>
+        <option value="sample_rate">sample_rate</option>
+      </param>
+      <param name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help="(-trace_termination_outliers) "/>
+      <param name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help="(-min_sample_rate) "/>
+      <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/>
+      <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/>
+      <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/>
+      <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/>
+      <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/>
+      <param name="param_algorithm_ffm_local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help="(-local_rt_range) "/>
+      <param name="param_algorithm_ffm_local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help="(-local_mz_range) "/>
+      <param name="param_algorithm_ffm_report_summed_ints" display="radio" type="boolean" truevalue="-algorithm:ffm:report_summed_ints" falsevalue="" checked="false" optional="True" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help="(-report_summed_ints) "/>
+      <param name="param_algorithm_ffm_use_smoothed_intensities" display="radio" type="select" optional="False" value="true" label="Use LOWESS intensities instead of raw intensities" help="(-use_smoothed_intensities) ">
+        <option value="false">false</option>
+        <option value="true" selected="true">true</option>
+      </param>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="featurexml"/>
+  </outputs>
+  <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
+</tool>