Mercurial > repos > galaxyp > openms_featurefindersuperhirn
diff FeatureFinderSuperHirn.xml @ 0:048af24c0e2b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
---|---|
date | Wed, 01 Mar 2017 12:23:05 -0500 |
parents | |
children | 6ef5f164d057 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FeatureFinderSuperHirn.xml Wed Mar 01 12:23:05 2017 -0500 @@ -0,0 +1,172 @@ +<?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="2.1.0"> + <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 +#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 $param_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 name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> + <param name="param_algorithm_centroiding_active" display="radio" type="boolean" truevalue="-algorithm:centroiding:active" falsevalue="" checked="false" optional="True" label="MS1 data centroid data" help="(-active) "/> + <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/> + <param name="param_algorithm_centroiding_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision) "/> + <param name="param_algorithm_centroiding_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision) "/> + <param name="param_algorithm_centroiding_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height) "/> + <param name="param_algorithm_centroiding_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity) "/> + <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels"> + <param name="param_algorithm_ms1_precursor_detection_scan_levels" type="text" size="30" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_ms1_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance) "/> + <param name="param_algorithm_ms1_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/> + <param name="param_algorithm_ms1_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold) "/> + <param name="param_algorithm_ms1_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance) "/> + <param name="param_algorithm_ms1_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members) "/> + <param name="param_algorithm_ms1_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope facto" help="(-detectable_isotope_factor) "/> + <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/> + <param name="param_algorithm_ms1_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance) "/> + <param name="param_algorithm_ms1_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance) "/> + <param name="param_algorithm_ms1_feature_merger_active" display="radio" type="select" optional="False" value="true" label="Activation of MS1 feature merging post processing" help="(-active) "> + <option value="true" selected="true">true</option> + <option value="false">false</option> + </param> + <param name="param_algorithm_ms1_feature_merger_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution) "/> + <param name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance) "/> + <param name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance) "/> + <param name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage) "/> + <param name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering) "/> + <param name="param_algorithm_ms1_feature_selection_options_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window) "/> + <param name="param_algorithm_ms1_feature_selection_options_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window) "/> + <param name="param_algorithm_ms1_feature_selection_options_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min) "/> + <param name="param_algorithm_ms1_feature_selection_options_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max) "/> + <param name="param_algorithm_ms1_feature_selection_options_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min) "/> + <param name="param_algorithm_ms1_feature_selection_options_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max) "/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="featurexml"/> + </outputs> + <help>Finds mass spectrometric features in mass spectra. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_FeatureFinderSuperHirn.html</help> +</tool>