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comparison FeatureFinderSuperHirn.xml @ 4:6ead64a594bd draft default tip

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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
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="1.12.0"> 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 <description>Finds mass spectrometric features in mass spectra.</description> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <macros> 4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.0.0">
5 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token> 5 <description>Finds mass spectrometric features in mass spectra.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>FeatureFinderSuperHirn 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FeatureFinderSuperHirn
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -threads \${GALAXY_SLOTS:-24} 17 #end if
15 ${param_active} 18 #if $param_out:
16 -algorithm:centroiding:window_width ${param_window_width} 19 -out $param_out
17 -algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision} 20 #end if
18 -algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision} 21 -threads \${GALAXY_SLOTS:-24}
19 -algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height} 22 #if $param_algorithm_centroiding_active:
20 -algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity} 23 -algorithm:centroiding:active
21 -algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels} 24 #end if
22 -algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance} 25 #if $param_algorithm_centroiding_window_width:
23 -algorithm:ms1:tr_resolution ${param_tr_resolution} 26 -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
24 -algorithm:ms1:intensity_threshold ${param_intensity_threshold} 27 #end if
25 -algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance} 28 #if $param_algorithm_centroiding_absolute_isotope_mass_precision:
26 -algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members} 29 -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
27 -algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor} 30 #end if
28 -algorithm:ms1:intensity_cv ${param_intensity_cv} 31 #if $param_algorithm_centroiding_relative_isotope_mass_precision:
29 -algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance} 32 -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
30 -algorithm:ms1:mz_tolerance ${param_mz_tolerance} 33 #end if
31 ${param_active} 34 #if $param_algorithm_centroiding_minimal_peak_height:
32 -algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution} 35 -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
33 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance} 36 #end if
34 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance} 37 #if $param_algorithm_centroiding_min_ms_signal_intensity:
35 -algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage} 38 -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
36 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering} 39 #end if
37 -algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window} 40
38 -algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window} 41 #if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
39 -algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min} 42 -algorithm:ms1:precursor_detection_scan_levels
40 -algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max} 43 #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
41 -algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min} 44 #if &quot; &quot; in str(token):
42 -algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max} 45 &quot;$token.param_algorithm_ms1_precursor_detection_scan_levels&quot;
46 #else
47 $token.param_algorithm_ms1_precursor_detection_scan_levels
48 #end if
49 #end for
50 #end if
51 #if $param_algorithm_ms1_max_inter_scan_distance:
52 -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
53 #end if
54 #if $param_algorithm_ms1_tr_resolution:
55 -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
56 #end if
57 #if $param_algorithm_ms1_intensity_threshold:
58 -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
59 #end if
60 #if $param_algorithm_ms1_max_inter_scan_rt_distance:
61 -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
62 #end if
63 #if $param_algorithm_ms1_min_nb_cluster_members:
64 -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
65 #end if
66 #if $param_algorithm_ms1_detectable_isotope_factor:
67 -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
68 #end if
69 #if $param_algorithm_ms1_intensity_cv:
70 -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
71 #end if
72 #if $param_algorithm_ms1_retention_time_tolerance:
73 -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
74 #end if
75 #if $param_algorithm_ms1_mz_tolerance:
76 -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
77 #end if
78 #if $param_algorithm_ms1_feature_merger_active:
79 -algorithm:ms1_feature_merger:active
80 #end if
81 #if $param_algorithm_ms1_feature_merger_tr_resolution:
82 -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
83 #end if
84 #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
85 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
86 #end if
87 #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
88 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
89 #end if
90 #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
91 -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
92 #end if
93 #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
94 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
95 #end if
96 #if $param_algorithm_ms1_feature_selection_options_start_elution_window:
97 -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
98 #end if
99 #if $param_algorithm_ms1_feature_selection_options_end_elution_window:
100 -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
101 #end if
102 #if $param_algorithm_ms1_feature_selection_options_mz_range_min:
103 -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
104 #end if
105 #if $param_algorithm_ms1_feature_selection_options_mz_range_max:
106 -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
107 #end if
108 #if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
109 -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
110 #end if
111 #if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
112 -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
113 #end if
114 #if $adv_opts.adv_opts_selector=='advanced':
115 #if $adv_opts.param_force:
116 -force
117 #end if
118 #end if
43 </command> 119 </command>
44 <inputs> 120 <inputs>
45 <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/> 121 <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/>
46 <param name="param_active" type="boolean" truevalue="-algorithm:centroiding:active true" falsevalue="-algorithm:centroiding:active false" checked="false" optional="True" label="MS1 data centroid data" help="(-active)"/> 122 <param checked="false" falsevalue="" help="(-active) " label="MS1 data centroid data" name="param_algorithm_centroiding_active" optional="True" truevalue="-algorithm:centroiding:active" type="boolean"/>
47 <param name="param_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width)"/> 123 <param help="(-window_width) " label="Centroid window width" min="1" name="param_algorithm_centroiding_window_width" optional="True" type="integer" value="5"/>
48 <param name="param_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 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"/>
49 <param name="param_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 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"/>
50 <param name="param_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height)"/> 126 <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"/>
51 <param name="param_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 <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"/>
52 <param name="param_precursor_detection_scan_levels" type="text" size="20" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels)"/> 128 <repeat max="1" min="0" name="rep_param_algorithm_ms1_precursor_detection_scan_levels" title="param_algorithm_ms1_precursor_detection_scan_levels">
53 <param name="param_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance)"/> 129 <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">
54 <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/> 130 <sanitizer>
55 <param name="param_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold)"/> 131 <valid initial="string.printable">
56 <param name="param_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)"/> 132 <remove value="'"/>
57 <param name="param_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)"/> 133 <remove value="&quot;"/>
58 <param name="param_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope factor" help="(-detectable_isotope_factor)"/> 134 </valid>
59 <param name="param_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv)"/> 135 </sanitizer>
60 <param name="param_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance)"/> 136 </param>
61 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance)"/> 137 </repeat>
62 <param name="param_active" type="boolean" truevalue="-algorithm:ms1_feature_merger:active true" falsevalue="-algorithm:ms1_feature_merger:active false" checked="true" optional="True" label="Activation of MS1 feature merging post processing" help="(-active)"/> 138 <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"/>
63 <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/> 139 <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"/>
64 <param name="param_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance)"/> 140 <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"/>
65 <param name="param_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)"/> 141 <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"/>
66 <param name="param_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)"/> 142 <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"/>
67 <param name="param_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)"/> 143 <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"/>
68 <param name="param_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window)"/> 144 <param help="(-intensity_cv) " label="IntensityCV" min="0.0" name="param_algorithm_ms1_intensity_cv" optional="True" type="float" value="0.9"/>
69 <param name="param_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window)"/> 145 <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"/>
70 <param name="param_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min)"/> 146 <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"/>
71 <param name="param_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max)"/> 147 <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"/>
72 <param name="param_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min)"/> 148 <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"/>
73 <param name="param_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max)"/> 149 <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"/>
74 </inputs> 150 <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"/>
75 <outputs> 151 <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"/>
76 <data name="param_out" label="output peak file " format="featureXML"/> 152 <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"/>
77 </outputs> 153 <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"/>
78 <help>**What it does** 154 <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"/>
79 155 <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"/>
80 Finds mass spectrometric features in mass spectra. 156 <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"/>
157 <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"/>
158 <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"/>
159 <expand macro="advanced_options">
160 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
161 </expand>
162 </inputs>
163 <outputs>
164 <data format="xml" name="param_out"/>
165 </outputs>
166 <help>Finds mass spectrometric features in mass spectra.
81 167
82 168
83 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html 169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html</help>
84 170 </tool>
85 @REFERENCES@
86 </help>
87 </tool>