annotate FeatureFinderSuperHirn.xml @ 13:6b6f5338c01c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:17:46 +0000
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Finds mass spectrometric features in mass spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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23 ## Main program call
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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31 -out
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32 'out/output.${gxy2omsext("featurexml")}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input profile data file" help=" select mzml data sets(s)"/>
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45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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46 <section name="centroiding" title="" help="" expanded="false">
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47 <param name="active" argument="-algorithm:centroiding:active" type="boolean" truevalue="true" falsevalue="false" checked="false" label="MS1 data centroid data" help=""/>
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48 <param name="window_width" argument="-algorithm:centroiding:window_width" type="integer" optional="true" min="1" value="5" label="Centroid window width" help=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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53 </section>
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54 <section name="ms1" title="" help="" expanded="false">
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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)">
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56 <expand macro="list_integer_valsan"/>
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57 </param>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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64 <param name="intensity_cv" argument="-algorithm:ms1:intensity_cv" type="float" optional="true" min="0.0" value="0.9" label="IntensityCV" help=""/>
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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=""/>
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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=""/>
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67 </section>
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68 <section name="ms1_feature_merger" title="" help="" expanded="false">
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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75 </section>
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76 <section name="ms1_feature_selection_options" title="" help="" expanded="false">
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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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=""/>
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83 </section>
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84 </section>
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85 <expand macro="adv_opts_macro">
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86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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88 <expand macro="list_string_san"/>
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89 </param>
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90 </expand>
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91 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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93 </param>
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94 </inputs>
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95 <outputs>
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96 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <expand macro="autotest_FeatureFinderSuperHirn"/>
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103 <expand macro="manutest_FeatureFinderSuperHirn"/>
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104 </tests>
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105 <help><![CDATA[Finds mass spectrometric features in mass spectra.
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106
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107
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108 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help>
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109 <expand macro="references"/>
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110 </tool>