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comparison FeatureFinderSuperHirn.xml @ 11:c42075bb5123 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 03 Sep 2020 16:16:49 +0000
parents f0ae67837629
children f35d5aa5d58a
comparison
equal deleted inserted replaced
10:cbb34edb8440 11:c42075bb5123
1 <?xml version='1.0' encoding='UTF-8'?> 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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.3.0"> 4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Finds mass spectrometric features in mass spectra.</description> 5 <description>Finds mass spectrometric features in mass spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token> 7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FeatureFinderSuperHirn 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir 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 22
40 #if $rep_param_algorithm_ms1_precursor_detection_scan_levels: 23 ## Main program call
41 -algorithm:ms1:precursor_detection_scan_levels 24
42 #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels: 25 set -o pipefail &&
43 #if " " in str(token): 26 @EXECUTABLE@ -write_ctd ./ &&
44 "$token.param_algorithm_ms1_precursor_detection_scan_levels" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
45 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
46 $token.param_algorithm_ms1_precursor_detection_scan_levels 29 -in
47 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
48 #end for 31 -out
49 #end if 32 'out/output.${gxy2omsext("featurexml")}'
50 #if $param_algorithm_ms1_max_inter_scan_distance: 33
51 -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance 34 ## Postprocessing
52 #end if 35 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
53 #if $param_algorithm_ms1_tr_resolution: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
54 -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
55 #end if 38 #end if]]></command>
56 #if $param_algorithm_ms1_intensity_threshold: 39 <configfiles>
57 -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold 40 <inputs name="args_json" data_style="paths"/>
58 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 #if $param_algorithm_ms1_max_inter_scan_rt_distance: 42 </configfiles>
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 $param_algorithm_ms1_feature_merger_active:
78 -algorithm:ms1_feature_merger:active
79 #if " " in str($param_algorithm_ms1_feature_merger_active):
80 "$param_algorithm_ms1_feature_merger_active"
81 #else
82 $param_algorithm_ms1_feature_merger_active
83 #end if
84 #end if
85 #if $param_algorithm_ms1_feature_merger_tr_resolution:
86 -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
87 #end if
88 #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
89 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
90 #end if
91 #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
92 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
93 #end if
94 #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
95 -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
96 #end if
97 #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
98 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
99 #end if
100 #if $param_algorithm_ms1_feature_selection_options_start_elution_window:
101 -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
102 #end if
103 #if $param_algorithm_ms1_feature_selection_options_end_elution_window:
104 -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
105 #end if
106 #if $param_algorithm_ms1_feature_selection_options_mz_range_min:
107 -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
108 #end if
109 #if $param_algorithm_ms1_feature_selection_options_mz_range_max:
110 -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
111 #end if
112 #if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
113 -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
114 #end if
115 #if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
116 -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
117 #end if
118 #if $adv_opts.adv_opts_selector=='advanced':
119 #if $adv_opts.param_force:
120 -force
121 #end if
122 #end if
123 ]]></command>
124 <inputs> 43 <inputs>
125 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
126 <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) "/> 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
127 <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/> 46 <section name="centroiding" title="" help="" expanded="false">
128 <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) "/> 47 <param name="active" argument="-algorithm:centroiding:active" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MS1 data centroid data" help=""/>
129 <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) "/> 48 <param name="window_width" argument="-algorithm:centroiding:window_width" type="integer" optional="true" min="1" value="5" label="Centroid window width" help=""/>
130 <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) "/> 49 <param name="absolute_isotope_mass_precision" argument="-algorithm:centroiding:absolute_isotope_mass_precision" type="float" optional="true" min="0.0" value="0.01" label="Absolute isotope mass precision (Da)" help=""/>
131 <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) "/> 50 <param name="relative_isotope_mass_precision" argument="-algorithm:centroiding:relative_isotope_mass_precision" type="float" optional="true" min="0.0" value="10.0" label="Relative isotope mass precision" help=""/>
132 <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels"> 51 <param name="minimal_peak_height" argument="-algorithm:centroiding:minimal_peak_height" type="float" optional="true" min="0.0" value="0.0" label="Minimal peak height" help=""/>
133 <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) "> 52 <param name="min_ms_signal_intensity" argument="-algorithm:centroiding:min_ms_signal_intensity" type="float" optional="true" min="0.0" value="50.0" label="Minimal Centroid MS Signal Intensity" help=""/>
134 <sanitizer> 53 </section>
135 <valid initial="string.printable"> 54 <section name="ms1" title="" help="" expanded="false">
136 <remove value="'"/> 55 <param name="precursor_detection_scan_levels" argument="-algorithm:ms1:precursor_detection_scan_levels" type="text" optional="true" value="1" label="Precursor detection scan levels" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
137 <remove value="&quot;"/> 56 <expand macro="list_integer_valsan"/>
138 </valid> 57 </param>
139 </sanitizer> 58 <param name="max_inter_scan_distance" argument="-algorithm:ms1:max_inter_scan_distance" type="integer" optional="true" min="0" value="0" label="MS1 max inter scan distance" help=""/>
59 <param name="tr_resolution" argument="-algorithm:ms1:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/>
60 <param name="intensity_threshold" argument="-algorithm:ms1:intensity_threshold" type="float" optional="true" min="0.0" value="1000.0" label="FT peak detect MS1 intensity min threshold" help=""/>
61 <param name="max_inter_scan_rt_distance" argument="-algorithm:ms1:max_inter_scan_rt_distance" type="float" optional="true" min="0.0" value="0.1" label="MS1 max inter scan distance" help=""/>
62 <param name="min_nb_cluster_members" argument="-algorithm:ms1:min_nb_cluster_members" type="integer" optional="true" min="0" value="4" label="FT peak detect MS1 min nb peak members" help=""/>
63 <param name="detectable_isotope_factor" argument="-algorithm:ms1:detectable_isotope_factor" type="float" optional="true" min="0.0" value="0.05" label="Detectable isotope facto" help=""/>
64 <param name="intensity_cv" argument="-algorithm:ms1:intensity_cv" type="float" optional="true" min="0.0" value="0.9" label="IntensityCV" help=""/>
65 <param name="retention_time_tolerance" argument="-algorithm:ms1:retention_time_tolerance" type="float" optional="true" min="0.0" value="0.5" label="MS1 retention time tolerance (minutes)" help=""/>
66 <param name="mz_tolerance" argument="-algorithm:ms1:mz_tolerance" type="float" optional="true" min="0.0" value="0.0" label="MS1 m/z tolerance (ppm)" help=""/>
67 </section>
68 <section name="ms1_feature_merger" title="" help="" expanded="false">
69 <param name="active" argument="-algorithm:ms1_feature_merger:active" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Activation of MS1 feature merging post processing" help=""/>
70 <param name="tr_resolution" argument="-algorithm:ms1_feature_merger:tr_resolution" type="float" optional="true" min="0.0" value="0.01" label="MS1 LC retention time resolution" help=""/>
71 <param name="initial_apex_tr_tolerance" argument="-algorithm:ms1_feature_merger:initial_apex_tr_tolerance" type="float" optional="true" min="0.0" value="5.0" label="Initial Apex Tr tolerance" help=""/>
72 <param name="feature_merging_tr_tolerance" argument="-algorithm:ms1_feature_merger:feature_merging_tr_tolerance" type="float" optional="true" min="0.0" value="1.0" label="MS1 feature Tr merging tolerance" help=""/>
73 <param name="intensity_variation_percentage" argument="-algorithm:ms1_feature_merger:intensity_variation_percentage" type="float" optional="true" min="0.0" max="100.0" value="25.0" label="Percentage of intensity variation between LC border peaks" help=""/>
74 <param name="ppm_tolerance_for_mz_clustering" argument="-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering" type="float" optional="true" min="0.0" value="10.0" label="PPM value for the m/z clustering of merging candidates" help=""/>
75 </section>
76 <section name="ms1_feature_selection_options" title="" help="" expanded="false">
77 <param name="start_elution_window" argument="-algorithm:ms1_feature_selection_options:start_elution_window" type="float" optional="true" min="0.0" value="0.0" label="start elution window (minutes)" help=""/>
78 <param name="end_elution_window" argument="-algorithm:ms1_feature_selection_options:end_elution_window" type="float" optional="true" min="0.0" value="180.0" label="end elution window (minutes)" help=""/>
79 <param name="mz_range_min" argument="-algorithm:ms1_feature_selection_options:mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="MS1 feature mz range min" help=""/>
80 <param name="mz_range_max" argument="-algorithm:ms1_feature_selection_options:mz_range_max" type="float" optional="true" min="0.0" value="2000.0" label="MS1 feature mz range max" help=""/>
81 <param name="chrg_range_min" argument="-algorithm:ms1_feature_selection_options:chrg_range_min" type="integer" optional="true" min="0" value="1" label="MS1 feature CHRG range min" help=""/>
82 <param name="chrg_range_max" argument="-algorithm:ms1_feature_selection_options:chrg_range_max" type="integer" optional="true" min="0" value="5" label="MS1 feature CHRG range max" help=""/>
83 </section>
84 </section>
85 <expand macro="adv_opts_macro">
86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
88 <expand macro="list_string_san"/>
140 </param> 89 </param>
141 </repeat> 90 </expand>
142 <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) "/> 91 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
143 <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) "/> 92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
144 <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) "/>
145 <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) "/>
146 <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) "/>
147 <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) "/>
148 <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/>
149 <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) "/>
150 <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) "/>
151 <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) ">
152 <option value="true" selected="true">true</option>
153 <option value="false">false</option>
154 </param> 93 </param>
155 <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) "/>
156 <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) "/>
157 <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) "/>
158 <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) "/>
159 <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) "/>
160 <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) "/>
161 <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) "/>
162 <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) "/>
163 <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) "/>
164 <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) "/>
165 <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) "/>
166 <expand macro="advanced_options">
167 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
168 </expand>
169 </inputs> 94 </inputs>
170 <outputs> 95 <outputs>
171 <data name="param_out" format="featurexml"/> 96 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
99 </data>
172 </outputs> 100 </outputs>
173 <help>Finds mass spectrometric features in mass spectra. 101 <tests>
102 <expand macro="autotest_FeatureFinderSuperHirn"/>
103 <expand macro="manutest_FeatureFinderSuperHirn"/>
104 </tests>
105 <help><![CDATA[Finds mass spectrometric features in mass spectra.
174 106
175 107 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_FeatureFinderSuperHirn.html]]></help>
176 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderSuperHirn.html</help> 108 <expand macro="references"/>
177 </tool> 109 </tool>