openms: FeatureFinderMetabo.xml comparison

comparison FeatureFinderMetabo.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

author	bgruening
date	Wed, 27 Jan 2016 10:06:49 -0500
parents	3d84209d3178
children

comparison

equal deleted inserted replaced

-:ec62782f6c68
+:6ead64a594bd
-<?xml version='1.0' encoding='UTF-8'?>
+<?xml version="1.0" encoding="UTF-8"?>
-<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="1.12.0">
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
-<description>Assembles metabolite features from singleton mass traces.</description>
+<!--Proposed Tool Section: [Quantitation]-->
-<macros>
+<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="2.0.0">
-<token name="@EXECUTABLE@">FeatureFinderMetabo</token>
+<description>Assembles metabolite features from singleton mass traces.</description>
-<import>macros.xml</import>
+<macros>
-</macros>
+<token name="@EXECUTABLE@">FeatureFinderMetabo</token>
-<expand macro="stdio"/>
+<import>macros.xml</import>
-<expand macro="requirements"/>
+</macros>
-<command>FeatureFinderMetabo
+<expand macro="references"/>
+<expand macro="stdio"/>
+<expand macro="requirements"/>
+<command>FeatureFinderMetabo
--in ${param_in}
+#if $param_in:
--out ${param_out}
+-in $param_in
--threads \${GALAXY_SLOTS:-24}
+#end if
--algorithm:common:noise_threshold_int ${param_noise_threshold_int}
+#if $param_out:
--algorithm:common:chrom_peak_snr ${param_chrom_peak_snr}
+-out $param_out
--algorithm:common:chrom_fwhm ${param_chrom_fwhm}
+#end if
--algorithm:mtd:mass_error_ppm ${param_mass_error_ppm}
+-threads \${GALAXY_SLOTS:-24}
-${param_reestimate_mt_sd}
+#if $param_algorithm_common_noise_threshold_int:
-${param_enabled}
+-algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
--algorithm:epd:width_filtering ${param_width_filtering}
+#end if
--algorithm:ffm:charge_lower_bound ${param_charge_lower_bound}
+#if $param_algorithm_common_chrom_peak_snr:
--algorithm:ffm:charge_upper_bound ${param_charge_upper_bound}
+-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_enabled:
+-algorithm:epd:enabled
+#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 $param_algorithm_ffm_quant_method:
+-algorithm:ffm:quant_method
+#if &quot; &quot; in str($param_algorithm_ffm_quant_method):
+&quot;$param_algorithm_ffm_quant_method&quot;
+#else
+$param_algorithm_ffm_quant_method
+#end if
+#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
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
--algorithm:mtd:trace_termination_criterion ${adv_opts.param_trace_termination_criterion}
+#if $adv_opts.param_force:
--algorithm:mtd:trace_termination_outliers ${adv_opts.param_trace_termination_outliers}
+-force
--algorithm:mtd:min_sample_rate ${adv_opts.param_min_sample_rate}
+#end if
--algorithm:mtd:min_trace_length ${adv_opts.param_min_trace_length}
+#if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
--algorithm:mtd:max_trace_length ${adv_opts.param_max_trace_length}
+-algorithm:mtd:trace_termination_criterion
--algorithm:epd:min_fwhm ${adv_opts.param_min_fwhm}
+#if &quot; &quot; in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
--algorithm:epd:max_fwhm ${adv_opts.param_max_fwhm}
+&quot;$adv_opts.param_algorithm_mtd_trace_termination_criterion&quot;
-${adv_opts.param_masstrace_snr_filtering}
+#else
--algorithm:ffm:local_rt_range ${adv_opts.param_local_rt_range}
+$adv_opts.param_algorithm_mtd_trace_termination_criterion
--algorithm:ffm:local_mz_range ${adv_opts.param_local_mz_range}
+#end if
-${adv_opts.param_report_summed_ints}
+#end if
-${adv_opts.param_disable_isotope_filtering}
+#if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
--algorithm:ffm:isotope_model ${adv_opts.param_isotope_model}
+-algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
--algorithm:ffm:isotope_noisemodel ${adv_opts.param_isotope_noisemodel}
+#end if
-${adv_opts.param_use_smoothed_intensities}
+#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_disable_isotope_filtering:
+-algorithm:ffm:disable_isotope_filtering
+#end if
+#if $adv_opts.param_algorithm_ffm_isotope_model:
+-algorithm:ffm:isotope_model
+#if &quot; &quot; in str($adv_opts.param_algorithm_ffm_isotope_model):
+&quot;$adv_opts.param_algorithm_ffm_isotope_model&quot;
+#else
+$adv_opts.param_algorithm_ffm_isotope_model
+#end if
+#end if
+#if $adv_opts.param_algorithm_ffm_isotope_noisemodel:
+-algorithm:ffm:isotope_noisemodel
+#if &quot; &quot; in str($adv_opts.param_algorithm_ffm_isotope_noisemodel):
+&quot;$adv_opts.param_algorithm_ffm_isotope_noisemodel&quot;
+#else
+$adv_opts.param_algorithm_ffm_isotope_noisemodel
+#end if
+#end if
+#if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
+-algorithm:ffm:use_smoothed_intensities
+#end if
 #end if
 </command>
 <inputs>
-<param name="param_in" type="data" format="mzML" optional="False" label="input centroided mzML file" help="(-in)"/>
+<param format="mzml" help="(-in) " label="Centroided mzML file" name="param_in" optional="False" type="data"/>
-<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 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 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 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 name="param_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)." help="(-chrom_fwhm)"/>
+<param help="(-chrom_fwhm) " label="Expected chromatographic peak width (in seconds)" name="param_algorithm_common_chrom_fwhm" type="float" value="5.0"/>
-<param name="param_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)." help="(-mass_error_ppm)"/>
+<param help="(-mass_error_ppm) " label="Allowed mass deviation (in ppm)" name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0"/>
-<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 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 name="param_enabled" type="boolean" truevalue="-algorithm:epd:enabled true" falsevalue="-algorithm:epd:enabled false" checked="true" optional="True" label="Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection." help="(-enabled)"/>
+<param checked="true" falsevalue="" help="(-enabled) Disable for direct injection" label="Enable splitting of isobaric mass traces by chromatographic peak detection" name="param_algorithm_epd_enabled" optional="True" truevalue="-algorithm:epd:enabled" type="boolean"/>
-<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)">
+<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_charge_lower_bound" type="integer" value="1" label="Lowest charge state to consider" help="(-charge_lower_bound)"/>
-<param name="param_charge_upper_bound" type="integer" value="3" label="Highest charge state to consider" help="(-charge_upper_bound)"/>
-<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>
 </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 help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data" label="Method of quantification for mass traces" name="param_algorithm_ffm_quant_method" optional="True" type="select" value="area">
-<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)"/>
+<option value="area">area</option>
-<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)"/>
+<option value="median">median</option>
-<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)"/>
-<param name="param_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_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_report_summed_ints" type="boolean" truevalue="-algorithm:ffm:report_summed_ints true" falsevalue="-algorithm:ffm:report_summed_ints false" 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_disable_isotope_filtering" type="boolean" truevalue="-algorithm:ffm:disable_isotope_filtering true" falsevalue="-algorithm:ffm:disable_isotope_filtering false" checked="false" optional="True" label="Disable isotope filtering." help="(-disable_isotope_filtering)"/>
-<param name="param_isotope_model" type="select" optional="True" value="metabolites" label="Change type of isotope model." help="(-isotope_model)">
-<option value="metabolites">metabolites</option>
-<option value="peptides">peptides</option>
 </param>
-<param name="param_isotope_noisemodel" type="select" optional="True" value="5%RMS" label="SVM isotope models were trained with either 2% or 5% RMS error. Select the appropriate noise model according to the quality of measurement or MS device." help="(-isotope_noisemodel)">
+<param help="(-charge_lower_bound) " label="Lowest charge state to conside" name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1"/>
-<option value="5%RMS">5%RMS</option>
+<param help="(-charge_upper_bound) " label="Highest charge state to conside" name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3"/>
-<option value="2%RMS">2%RMS</option>
+<param checked="true" falsevalue="" help="(-enable_RT_filtering) Disable for direct injection data" label="Require sufficient overlap in RT while assembling mass traces" name="param_algorithm_ffm_enable_RT_filtering" optional="True" truevalue="-algorithm:ffm:enable_RT_filtering" type="boolean"/>
-</param>
+<expand macro="advanced_options">
-<param name="param_use_smoothed_intensities" type="boolean" truevalue="-algorithm:ffm:use_smoothed_intensities true" falsevalue="-algorithm:ffm:use_smoothed_intensities false" checked="true" optional="True" label="Use LOWESS intensities instead of raw intensities." help="(-use_smoothed_intensities)"/>
+<param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
-</expand>
+<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">
-</inputs>
+<option value="outlier">outlier</option>
-<outputs>
+<option value="sample_rate">sample_rate</option>
-<data name="param_out" label="output featureXML file with metabolite features" format="featureXML"/>
+</param>
-</outputs>
+<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"/>
-<help>**What it does**
+<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"/>
-Assembles metabolite features from singleton mass traces.
+<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"/>
+<param help="(-local_rt_range) " label="RT range where to look for coeluting mass traces" name="param_algorithm_ffm_local_rt_range" type="float" value="10.0"/>
+<param help="(-local_mz_range) " label="MZ range where to look for isotopic mass traces" name="param_algorithm_ffm_local_mz_range" type="float" value="6.5"/>
+<param checked="false" falsevalue="" help="(-report_summed_ints) " label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" name="param_algorithm_ffm_report_summed_ints" optional="True" truevalue="-algorithm:ffm:report_summed_ints" type="boolean"/>
+<param checked="false" falsevalue="" help="(-disable_isotope_filtering) " label="Disable isotope filtering" name="param_algorithm_ffm_disable_isotope_filtering" optional="True" truevalue="-algorithm:ffm:disable_isotope_filtering" type="boolean"/>
+<param help="(-isotope_model) " label="Change type of isotope model" name="param_algorithm_ffm_isotope_model" optional="True" type="select" value="metabolites">
+<option value="metabolites">metabolites</option>
+<option value="peptides">peptides</option>
+</param>
+<param help="(-isotope_noisemodel) Select the appropriate noise model according to the quality of measurement or MS device" label="SVM isotope models were trained with either 2% or 5% RMS erro" name="param_algorithm_ffm_isotope_noisemodel" optional="True" type="select" value="5%RMS">
+<option value="5%RMS">5%RMS</option>
+<option value="2%RMS">2%RMS</option>
+</param>
+<param checked="true" falsevalue="" help="(-use_smoothed_intensities) " label="Use LOWESS intensities instead of raw intensities" name="param_algorithm_ffm_use_smoothed_intensities" optional="True" truevalue="-algorithm:ffm:use_smoothed_intensities" type="boolean"/>
+</expand>
+</inputs>
+<outputs>
+<data format="xml" name="param_out"/>
+</outputs>
+<help>Assembles metabolite features from singleton mass traces.
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
+</tool>
-@REFERENCES@
-</help>
-</tool>

Mercurial > repos > bgruening > openms

comparison FeatureFinderMetabo.xml @ 4:6ead64a594bd draft default tip