--- a/MassTraceExtractor.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/MassTraceExtractor.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,81 +1,130 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="MassTraceExtractor" name="MassTraceExtractor" version="1.12.0">
-  <description>Detects mass traces in centroided LC-MS data.</description>
-  <macros>
-    <token name="@EXECUTABLE@">MassTraceExtractor</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MassTraceExtractor
+<?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: [Signal processing and preprocessing]-->
+  <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.0.0">
+    <description>Detects mass traces in centroided LC-MS data.</description>
+    <macros>
+      <token name="@EXECUTABLE@">MassTraceExtractor</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>MassTraceExtractor
 
--in ${param_in}
--out ${param_out}
--out_type ${param_out_type}
--threads \${GALAXY_SLOTS:-24} 
--algorithm:common:noise_threshold_int ${param_noise_threshold_int}
--algorithm:common:chrom_peak_snr ${param_chrom_peak_snr}
--algorithm:common:chrom_fwhm ${param_chrom_fwhm}
--algorithm:mtd:mass_error_ppm ${param_mass_error_ppm}
-${param_reestimate_mt_sd}
--algorithm:epd:width_filtering ${param_width_filtering}
-${param_enabled}
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_type:
+  -out_type
+  #if &quot; &quot; in str($param_out_type):
+    &quot;$param_out_type&quot;
+  #else
+    $param_out_type
+  #end if
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#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
+#end if
+#if $param_algorithm_epd_width_filtering:
+  -algorithm:epd:width_filtering
+  #if &quot; &quot; in str($param_algorithm_epd_width_filtering):
+    &quot;$param_algorithm_epd_width_filtering&quot;
+  #else
+    $param_algorithm_epd_width_filtering
+  #end if
+#end if
+#if $param_algorithm_epd_enabled:
+  -algorithm:epd:enabled
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
-    -algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion}
-    -algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers}
-    -algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate}
-    -algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length}
-    -algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length}
-    -algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm}
-    -algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm}
-    ${adv_opts.param_masstrace_snr_filtering}
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
+  -algorithm:mtd:trace_termination_criterion
+  #if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
+    &quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
+  #else
+    $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  #end if
+#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
 #end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="input centroided mzML file" help="(-in)"/>
-    <param name="param_out_type" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type)">
-      <option value="featureXML">featureXML</option>
-      <option value="consensusXML">consensusXML</option>
-    </param>
-    <param name="param_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_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_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)." help="(-chrom_fwhm)"/>
-    <param name="param_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)." help="(-mass_error_ppm)"/>
-    <param name="param_reestimate_mt_sd" type="boolean" truevalue="-algorithm:mtd:reestimate_mt_sd true" falsevalue="-algorithm:mtd:reestimate_mt_sd false" checked="true" optional="True" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage." help="(-reestimate_mt_sd)"/>
-    <param name="param_width_filtering" type="select" optional="True" value="fixed" label="Enable filtering of unlikely peak widths. 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." help="(-width_filtering)">
-      <option value="off">off</option>
-      <option value="fixed">fixed</option>
-      <option value="auto">auto</option>
-    </param>
-    <param name="param_enabled" type="boolean" truevalue="-algorithm:epd:enabled true" falsevalue="-algorithm:epd:enabled false" checked="true" optional="True" label="Enables/disables the chromatographic peak detection of mass traces" help="(-enabled)"/>
-    <expand macro="advanced_options">
-      <param name="param_trace_termination_criterion" type="select" optional="True" value="outlier" label="Termination criterion for the extension of mass traces. 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." help="(-trace_termination_criterion)">
-        <option value="outlier">outlier</option>
-        <option value="sample_rate">sample_rate</option>
+    <inputs>
+      <param format="mzml" help="(-in) " label="input centroided mzML file" name="param_in" optional="False" type="data"/>
+      <param help="(-out_type) " label="output file type -- default: determined from file extension or content" name="param_out_type" optional="True" type="select">
+        <option value="featureXML">featureXML</option>
+        <option value="consensusXML">consensusXML</option>
+      </param>
+      <param help="(-noise_threshold_int) " label="Intensity threshold below which peaks are regarded as noise" name="param_algorithm_common_noise_threshold_int" type="float" value="10.0"/>
+      <param help="(-chrom_peak_snr) " label="Minimum signal-to-noise a mass trace should have" name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0"/>
+      <param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
+      <param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
+      <param checked="true" falsevalue="" help="(-reestimate_mt_sd) " label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" name="param_algorithm_mtd_reestimate_mt_sd" optional="True" truevalue="-algorithm:mtd:reestimate_mt_sd" type="boolean"/>
+      <param 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" label="Enable filtering of unlikely peak widths" name="param_algorithm_epd_width_filtering" optional="True" type="select" value="fixed">
+        <option value="off">off</option>
+        <option value="fixed">fixed</option>
+        <option value="auto">auto</option>
       </param>
-      <param name="param_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_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_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_max_trace_length" type="float" value="300.0" label="Minimum expected length of a mass trace (in seconds)." help="(-max_trace_length)"/>
-      <param name="param_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-min_fwhm)"/>
-      <param name="param_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if paramter width_filtering is off or auto." help="(-max_fwhm)"/>
-      <param name="param_masstrace_snr_filtering" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering true" falsevalue="-algorithm:epd:masstrace_snr_filtering false" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing." help="(-masstrace_snr_filtering)"/>
-    </expand>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output featureXML file with mass traces" format="consensusXML">
-      <change_format>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-      </change_format>
-    </data>
-  </outputs>
-  <help>**What it does**
-
-Detects mass traces in centroided LC-MS data.
+      <param checked="true" falsevalue="" help="(-enabled) " label="Enables/disables the chromatographic peak detection of mass traces" name="param_algorithm_epd_enabled" optional="True" truevalue="-algorithm:epd:enabled" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param 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" label="Termination criterion for the extension of mass traces" name="param_algorithm_mtd_trace_termination_criterion" optional="True" type="select" value="outlier">
+          <option value="outlier">outlier</option>
+          <option value="sample_rate">sample_rate</option>
+        </param>
+        <param help="(-trace_termination_outliers) " label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5"/>
+        <param help="(-min_sample_rate) " label="Minimum fraction of scans along the mass trace that must contain a peak" name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5"/>
+        <param help="(-min_trace_length) " label="Minimum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_min_trace_length" type="float" value="5.0"/>
+        <param help="(-max_trace_length) " label="Maximum expected length of a mass trace (in seconds)" name="param_algorithm_mtd_max_trace_length" type="float" value="300.0"/>
+        <param help="(-min_fwhm) Ignored if parameter width_filtering is off or auto" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_min_fwhm" type="float" value="3.0"/>
+        <param help="(-max_fwhm) Ignored if parameter width_filtering is off or auto" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" name="param_algorithm_epd_max_fwhm" type="float" value="60.0"/>
+        <param checked="false" falsevalue="" help="(-masstrace_snr_filtering) " label="Apply post-filtering by signal-to-noise ratio after smoothing" name="param_algorithm_epd_masstrace_snr_filtering" optional="True" truevalue="-algorithm:epd:masstrace_snr_filtering" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="xml" name="param_out"/>
+    </outputs>
+    <help>Detects mass traces in centroided LC-MS data.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MassTraceExtractor.html</help>
+  </tool>