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view FeatureFinderSuperHirn.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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<?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="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.0.0"> <description>Finds mass spectrometric features in mass spectra.</description> <macros> <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>FeatureFinderSuperHirn #if $param_in: -in $param_in #end if #if $param_out: -out $param_out #end if -threads \${GALAXY_SLOTS:-24} #if $param_algorithm_centroiding_active: -algorithm:centroiding:active #end if #if $param_algorithm_centroiding_window_width: -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width #end if #if $param_algorithm_centroiding_absolute_isotope_mass_precision: -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision #end if #if $param_algorithm_centroiding_relative_isotope_mass_precision: -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision #end if #if $param_algorithm_centroiding_minimal_peak_height: -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height #end if #if $param_algorithm_centroiding_min_ms_signal_intensity: -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity #end if #if $rep_param_algorithm_ms1_precursor_detection_scan_levels: -algorithm:ms1:precursor_detection_scan_levels #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels: #if " " in str(token): "$token.param_algorithm_ms1_precursor_detection_scan_levels" #else $token.param_algorithm_ms1_precursor_detection_scan_levels #end if #end for #end if #if $param_algorithm_ms1_max_inter_scan_distance: -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance #end if #if $param_algorithm_ms1_tr_resolution: -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution #end if #if $param_algorithm_ms1_intensity_threshold: -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold #end if #if $param_algorithm_ms1_max_inter_scan_rt_distance: -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance #end if #if $param_algorithm_ms1_min_nb_cluster_members: -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members #end if #if $param_algorithm_ms1_detectable_isotope_factor: -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor #end if #if $param_algorithm_ms1_intensity_cv: -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv #end if #if $param_algorithm_ms1_retention_time_tolerance: -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance #end if #if $param_algorithm_ms1_mz_tolerance: -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance #end if #if $param_algorithm_ms1_feature_merger_active: -algorithm:ms1_feature_merger:active #end if #if $param_algorithm_ms1_feature_merger_tr_resolution: -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution #end if #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance: -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance #end if #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance: -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance #end if #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage: -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage #end if #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering: -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering #end if #if $param_algorithm_ms1_feature_selection_options_start_elution_window: -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window #end if #if $param_algorithm_ms1_feature_selection_options_end_elution_window: -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window #end if #if $param_algorithm_ms1_feature_selection_options_mz_range_min: -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min #end if #if $param_algorithm_ms1_feature_selection_options_mz_range_max: -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max #end if #if $param_algorithm_ms1_feature_selection_options_chrg_range_min: -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min #end if #if $param_algorithm_ms1_feature_selection_options_chrg_range_max: -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/> <param checked="false" falsevalue="" help="(-active) " label="MS1 data centroid data" name="param_algorithm_centroiding_active" optional="True" truevalue="-algorithm:centroiding:active" type="boolean"/> <param help="(-window_width) " label="Centroid window width" min="1" name="param_algorithm_centroiding_window_width" optional="True" type="integer" value="5"/> <param help="(-absolute_isotope_mass_precision) " label="Absolute isotope mass precision (Da)" min="0.0" name="param_algorithm_centroiding_absolute_isotope_mass_precision" optional="True" type="float" value="0.01"/> <param help="(-relative_isotope_mass_precision) " label="Relative isotope mass precision" min="0.0" name="param_algorithm_centroiding_relative_isotope_mass_precision" optional="True" type="float" value="10.0"/> <param help="(-minimal_peak_height) " label="Minimal peak height" min="0.0" name="param_algorithm_centroiding_minimal_peak_height" optional="True" type="float" value="0.0"/> <param help="(-min_ms_signal_intensity) " label="Minimal Centroid MS Signal Intensity" min="0.0" name="param_algorithm_centroiding_min_ms_signal_intensity" optional="True" type="float" value="50.0"/> <repeat max="1" min="0" name="rep_param_algorithm_ms1_precursor_detection_scan_levels" title="param_algorithm_ms1_precursor_detection_scan_levels"> <param help="(-precursor_detection_scan_levels) " label="Precursor detection scan levels" name="param_algorithm_ms1_precursor_detection_scan_levels" size="30" type="text" value="1"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> </repeat> <param help="(-max_inter_scan_distance) " label="MS1 max inter scan distance" min="0" name="param_algorithm_ms1_max_inter_scan_distance" optional="True" type="integer" value="0"/> <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_tr_resolution" optional="True" type="float" value="0.01"/> <param help="(-intensity_threshold) " label="FT peak detect MS1 intensity min threshold" min="0.0" name="param_algorithm_ms1_intensity_threshold" optional="True" type="float" value="1000.0"/> <param help="(-max_inter_scan_rt_distance) " label="MS1 max inter scan distance" min="0.0" name="param_algorithm_ms1_max_inter_scan_rt_distance" optional="True" type="float" value="0.1"/> <param help="(-min_nb_cluster_members) " label="FT peak detect MS1 min nb peak members" min="0" name="param_algorithm_ms1_min_nb_cluster_members" optional="True" type="integer" value="4"/> <param help="(-detectable_isotope_factor) " label="Detectable isotope facto" min="0.0" name="param_algorithm_ms1_detectable_isotope_factor" optional="True" type="float" value="0.05"/> <param help="(-intensity_cv) " label="IntensityCV" min="0.0" name="param_algorithm_ms1_intensity_cv" optional="True" type="float" value="0.9"/> <param help="(-retention_time_tolerance) " label="MS1 retention time tolerance (minutes)" min="0.0" name="param_algorithm_ms1_retention_time_tolerance" optional="True" type="float" value="0.5"/> <param help="(-mz_tolerance) " label="MS1 m/z tolerance (ppm)" min="0.0" name="param_algorithm_ms1_mz_tolerance" optional="True" type="float" value="0.0"/> <param checked="true" falsevalue="" help="(-active) " label="Activation of MS1 feature merging post processing" name="param_algorithm_ms1_feature_merger_active" optional="True" truevalue="-algorithm:ms1_feature_merger:active" type="boolean"/> <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_feature_merger_tr_resolution" optional="True" type="float" value="0.01"/> <param help="(-initial_apex_tr_tolerance) " label="Initial Apex Tr tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" optional="True" type="float" value="5.0"/> <param help="(-feature_merging_tr_tolerance) " label="MS1 feature Tr merging tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" optional="True" type="float" value="1.0"/> <param help="(-intensity_variation_percentage) " label="Percentage of intensity variation between LC border peaks" max="100.0" min="0.0" name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" optional="True" type="float" value="25.0"/> <param help="(-ppm_tolerance_for_mz_clustering) " label="PPM value for the m/z clustering of merging candidates" min="0.0" name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" optional="True" type="float" value="10.0"/> <param help="(-start_elution_window) " label="start elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_start_elution_window" optional="True" type="float" value="0.0"/> <param help="(-end_elution_window) " label="end elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_end_elution_window" optional="True" type="float" value="180.0"/> <param help="(-mz_range_min) " label="MS1 feature mz range min" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_min" optional="True" type="float" value="0.0"/> <param help="(-mz_range_max) " label="MS1 feature mz range max" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_max" optional="True" type="float" value="2000.0"/> <param help="(-chrg_range_min) " label="MS1 feature CHRG range min" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_min" optional="True" type="integer" value="1"/> <param help="(-chrg_range_max) " label="MS1 feature CHRG range max" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_max" optional="True" type="integer" value="5"/> <expand macro="advanced_options"> <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/> </expand> </inputs> <outputs> <data format="xml" name="param_out"/> </outputs> <help>Finds mass spectrometric features in mass spectra. For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html</help> </tool>