Mercurial > repos > galaxyp > openms_featurefindersuperhirn
comparison 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 |
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| -1:000000000000 | 0:048af24c0e2b |
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| 1 <?xml version='1.0' encoding='UTF-8'?> | |
| 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [Quantitation]--> | |
| 4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.1.0"> | |
| 5 <description>Finds mass spectrometric features in mass spectra.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>FeatureFinderSuperHirn | |
| 14 | |
| 15 #if $param_in: | |
| 16 -in $param_in | |
| 17 #end if | |
| 18 #if $param_out: | |
| 19 -out $param_out | |
| 20 #end if | |
| 21 #if $param_algorithm_centroiding_active: | |
| 22 -algorithm:centroiding:active | |
| 23 #end if | |
| 24 #if $param_algorithm_centroiding_window_width: | |
| 25 -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width | |
| 26 #end if | |
| 27 #if $param_algorithm_centroiding_absolute_isotope_mass_precision: | |
| 28 -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision | |
| 29 #end if | |
| 30 #if $param_algorithm_centroiding_relative_isotope_mass_precision: | |
| 31 -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision | |
| 32 #end if | |
| 33 #if $param_algorithm_centroiding_minimal_peak_height: | |
| 34 -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height | |
| 35 #end if | |
| 36 #if $param_algorithm_centroiding_min_ms_signal_intensity: | |
| 37 -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity | |
| 38 #end if | |
| 39 | |
| 40 #if $rep_param_algorithm_ms1_precursor_detection_scan_levels: | |
| 41 -algorithm:ms1:precursor_detection_scan_levels | |
| 42 #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels: | |
| 43 #if " " in str(token): | |
| 44 "$token.param_algorithm_ms1_precursor_detection_scan_levels" | |
| 45 #else | |
| 46 $token.param_algorithm_ms1_precursor_detection_scan_levels | |
| 47 #end if | |
| 48 #end for | |
| 49 #end if | |
| 50 #if $param_algorithm_ms1_max_inter_scan_distance: | |
| 51 -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance | |
| 52 #end if | |
| 53 #if $param_algorithm_ms1_tr_resolution: | |
| 54 -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution | |
| 55 #end if | |
| 56 #if $param_algorithm_ms1_intensity_threshold: | |
| 57 -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold | |
| 58 #end if | |
| 59 #if $param_algorithm_ms1_max_inter_scan_rt_distance: | |
| 60 -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance | |
| 61 #end if | |
| 62 #if $param_algorithm_ms1_min_nb_cluster_members: | |
| 63 -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members | |
| 64 #end if | |
| 65 #if $param_algorithm_ms1_detectable_isotope_factor: | |
| 66 -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor | |
| 67 #end if | |
| 68 #if $param_algorithm_ms1_intensity_cv: | |
| 69 -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv | |
| 70 #end if | |
| 71 #if $param_algorithm_ms1_retention_time_tolerance: | |
| 72 -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance | |
| 73 #end if | |
| 74 #if $param_algorithm_ms1_mz_tolerance: | |
| 75 -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance | |
| 76 #end if | |
| 77 #if $param_algorithm_ms1_feature_merger_active: | |
| 78 -algorithm:ms1_feature_merger:active $param_algorithm_ms1_feature_merger_active | |
| 79 #end if | |
| 80 #if $param_algorithm_ms1_feature_merger_tr_resolution: | |
| 81 -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution | |
| 82 #end if | |
| 83 #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance: | |
| 84 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance | |
| 85 #end if | |
| 86 #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance: | |
| 87 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance | |
| 88 #end if | |
| 89 #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage: | |
| 90 -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage | |
| 91 #end if | |
| 92 #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering: | |
| 93 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering | |
| 94 #end if | |
| 95 #if $param_algorithm_ms1_feature_selection_options_start_elution_window: | |
| 96 -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window | |
| 97 #end if | |
| 98 #if $param_algorithm_ms1_feature_selection_options_end_elution_window: | |
| 99 -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window | |
| 100 #end if | |
| 101 #if $param_algorithm_ms1_feature_selection_options_mz_range_min: | |
| 102 -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min | |
| 103 #end if | |
| 104 #if $param_algorithm_ms1_feature_selection_options_mz_range_max: | |
| 105 -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max | |
| 106 #end if | |
| 107 #if $param_algorithm_ms1_feature_selection_options_chrg_range_min: | |
| 108 -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min | |
| 109 #end if | |
| 110 #if $param_algorithm_ms1_feature_selection_options_chrg_range_max: | |
| 111 -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max | |
| 112 #end if | |
| 113 #if $adv_opts.adv_opts_selector=='advanced': | |
| 114 #if $adv_opts.param_force: | |
| 115 -force | |
| 116 #end if | |
| 117 #end if | |
| 118 </command> | |
| 119 <inputs> | |
| 120 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> | |
| 121 <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) "/> | |
| 122 <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/> | |
| 123 <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) "/> | |
| 124 <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) "/> | |
| 125 <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) "/> | |
| 126 <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) "/> | |
| 127 <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels"> | |
| 128 <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) "> | |
| 129 <sanitizer> | |
| 130 <valid initial="string.printable"> | |
| 131 <remove value="'"/> | |
| 132 <remove value="""/> | |
| 133 </valid> | |
| 134 </sanitizer> | |
| 135 </param> | |
| 136 </repeat> | |
| 137 <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) "/> | |
| 138 <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) "/> | |
| 139 <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) "/> | |
| 140 <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) "/> | |
| 141 <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) "/> | |
| 142 <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) "/> | |
| 143 <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/> | |
| 144 <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) "/> | |
| 145 <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) "/> | |
| 146 <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) "> | |
| 147 <option value="true" selected="true">true</option> | |
| 148 <option value="false">false</option> | |
| 149 </param> | |
| 150 <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) "/> | |
| 151 <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) "/> | |
| 152 <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) "/> | |
| 153 <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) "/> | |
| 154 <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) "/> | |
| 155 <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) "/> | |
| 156 <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) "/> | |
| 157 <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) "/> | |
| 158 <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) "/> | |
| 159 <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) "/> | |
| 160 <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) "/> | |
| 161 <expand macro="advanced_options"> | |
| 162 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | |
| 163 </expand> | |
| 164 </inputs> | |
| 165 <outputs> | |
| 166 <data name="param_out" format="featurexml"/> | |
| 167 </outputs> | |
| 168 <help>Finds mass spectrometric features in mass spectra. | |
| 169 | |
| 170 | |
| 171 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_FeatureFinderSuperHirn.html</help> | |
| 172 </tool> |