Mercurial > repos > bgruening > openms
diff 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 |
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--- a/FeatureFinderMetabo.xml Mon Oct 13 10:18:22 2014 -0400 +++ b/FeatureFinderMetabo.xml Wed Jan 27 10:06:49 2016 -0500 @@ -1,96 +1,186 @@ -<?xml version='1.0' encoding='UTF-8'?> -<tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="1.12.0"> - <description>Assembles metabolite features from singleton mass traces.</description> - <macros> - <token name="@EXECUTABLE@">FeatureFinderMetabo</token> - <import>macros.xml</import> - </macros> - <expand macro="stdio"/> - <expand macro="requirements"/> - <command>FeatureFinderMetabo +<?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="2.0.0"> + <description>Assembles metabolite features from singleton mass traces.</description> + <macros> + <token name="@EXECUTABLE@">FeatureFinderMetabo</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>FeatureFinderMetabo --in ${param_in} --out ${param_out} --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} -${param_enabled} --algorithm:epd:width_filtering ${param_width_filtering} --algorithm:ffm:charge_lower_bound ${param_charge_lower_bound} --algorithm:ffm:charge_upper_bound ${param_charge_upper_bound} +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#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_enabled: + -algorithm:epd:enabled +#end if +#if $param_algorithm_epd_width_filtering: + -algorithm:epd:width_filtering + #if " " in str($param_algorithm_epd_width_filtering): + "$param_algorithm_epd_width_filtering" + #else + $param_algorithm_epd_width_filtering + #end if +#end if +#if $param_algorithm_ffm_quant_method: + -algorithm:ffm:quant_method + #if " " in str($param_algorithm_ffm_quant_method): + "$param_algorithm_ffm_quant_method" + #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} - -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} - -algorithm:ffm:local_rt_range ${adv_opts.param_local_rt_range} - -algorithm:ffm:local_mz_range ${adv_opts.param_local_mz_range} - ${adv_opts.param_report_summed_ints} - ${adv_opts.param_disable_isotope_filtering} - -algorithm:ffm:isotope_model ${adv_opts.param_isotope_model} - -algorithm:ffm:isotope_noisemodel ${adv_opts.param_isotope_noisemodel} - ${adv_opts.param_use_smoothed_intensities} + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: + -algorithm:mtd:trace_termination_criterion + #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): + "$adv_opts.param_algorithm_mtd_trace_termination_criterion" + #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 + #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 $adv_opts.param_algorithm_ffm_isotope_model: + -algorithm:ffm:isotope_model + #if " " in str($adv_opts.param_algorithm_ffm_isotope_model): + "$adv_opts.param_algorithm_ffm_isotope_model" + #else + $adv_opts.param_algorithm_ffm_isotope_model + #end if +#end if + #if $adv_opts.param_algorithm_ffm_isotope_noisemodel: + -algorithm:ffm:isotope_noisemodel + #if " " in str($adv_opts.param_algorithm_ffm_isotope_noisemodel): + "$adv_opts.param_algorithm_ffm_isotope_noisemodel" + #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 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_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 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_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> + <inputs> + <param format="mzml" help="(-in) " label="Centroided mzML file" name="param_in" optional="False" type="data"/> + <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 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 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 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"> + <option value="area">area</option> + <option value="median">median</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)"/> - <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)"> - <option value="5%RMS">5%RMS</option> - <option value="2%RMS">2%RMS</option> - </param> - <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)"/> - </expand> - </inputs> - <outputs> - <data name="param_out" label="output featureXML file with metabolite features" format="featureXML"/> - </outputs> - <help>**What it does** - -Assembles metabolite features from singleton mass traces. + <param help="(-charge_lower_bound) " label="Lowest charge state to conside" name="param_algorithm_ffm_charge_lower_bound" type="integer" value="1"/> + <param help="(-charge_upper_bound) " label="Highest charge state to conside" name="param_algorithm_ffm_charge_upper_bound" type="integer" value="3"/> + <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"/> + <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"/> + <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 - -@REFERENCES@ -</help> -</tool> +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help> + </tool>