Mercurial > repos > bgruening > openms
view 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 |
line wrap: on
line source
<?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 #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': #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 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 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</help> </tool>