Mercurial > repos > galaxyp > openms_featurefinderidentification

annotate FeatureFinderIdentification.xml @ 16:65bdfab68571 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:29 +0000
parents 5dc928c83939
children
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39ccf2ebfe49 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--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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2 <!--Proposed Tool Section: [Quantitation]-->
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3 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Detects features in MS1 data based on peptide identifications</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">FeatureFinderIdentification</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in &&
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65bdfab68571 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir id &&
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19 cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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20 #if $id_ext:
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21 mkdir id_ext &&
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22 cp '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
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23 #end if
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24 mkdir out &&
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25 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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26 mkdir lib_out &&
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27 #end if
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28 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir chrom_out &&
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30 #end if
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31 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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32 mkdir candidates_out &&
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33 #end if
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34 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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35 mkdir svm_xval_out &&
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36 #end if
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37 ## advanced options
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38 #if $adv_opts.candidates_in:
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39 mkdir adv_opts.candidates_in &&
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40 cp '$adv_opts.candidates_in' 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)' &&
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c040ffc3ac9b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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41 #end if
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42
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43
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44 ## Main program call
3
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45
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46 set -o pipefail &&
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47 @EXECUTABLE@ -write_ctd ./ &&
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48 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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49 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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50 -in
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51 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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52 -id
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53 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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54 #if $id_ext:
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55 -id_ext
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56 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)'
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57 #end if
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58 -out
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59 'out/output.${gxy2omsext("featurexml")}'
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60 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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61 -lib_out
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62 'lib_out/output.${gxy2omsext("traml")}'
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63 #end if
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64 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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65 -chrom_out
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66 'chrom_out/output.${gxy2omsext("mzml")}'
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67 #end if
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68 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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69 -candidates_out
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70 'candidates_out/output.${gxy2omsext("featurexml")}'
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71 #end if
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72 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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73 -svm:xval_out
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74 'svm_xval_out/output.${gxy2omsext("csv")}'
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75 #end if
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76 ## advanced options
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77 #if $adv_opts.candidates_in:
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78 -candidates_in
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79 'adv_opts.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts.candidates_in.element_identifier)}.$gxy2omsext($adv_opts.candidates_in.ext)'
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80 #end if
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81
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82 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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83 | tee '$stdout'
3
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84 #end if
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85
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86 ## Postprocessing
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87 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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88 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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89 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
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90 #end if
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91 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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92 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
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93 #end if
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94 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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95 && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
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96 #end if
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97 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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98 && mv 'svm_xval_out/output.${gxy2omsext("csv")}' '$svm_xval_out'
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99 #end if
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100 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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101 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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102 #end if]]></command>
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103 <configfiles>
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104 <inputs name="args_json" data_style="paths"/>
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105 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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106 </configfiles>
0
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107 <inputs>
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108 <param argument="-in" type="data" format="mzml" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
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109 <param argument="-id" type="data" format="idxml" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
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110 <param argument="-id_ext" type="data" format="idxml" optional="true" label="Input file: 'External' peptide identifications" help="(e.g. from aligned runs) select idxml data sets(s)"/>
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111 <param argument="-quantify_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether decoy peptides should be quantified (true) or skipped (false)" help=""/>
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112 <param argument="-min_psm_cutoff" type="text" value="none" label="Minimum score for the best PSM of a spectrum to be used as seed" help="Use 'none' for no cutoff">
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113 <expand macro="list_string_san" name="min_psm_cutoff"/>
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114 </param>
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115 <param argument="-add_mass_offset_peptides" type="float" min="0.0" value="0.0" label="If for every peptide (or seed) also an offset peptide is extracted (true)" help="Can be used to downstream to determine MBR false transfer rates. (0.0 = disabled)"/>
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116 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
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117 <param name="batch_size" argument="-extract:batch_size" type="integer" min="1" value="5000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
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118 <param name="mz_window" argument="-extract:mz_window" type="float" min="0.0" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help=""/>
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119 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
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120 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="If set, this parameter takes precedence over 'extract:n_isotopes'"/>
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121 <param name="rt_quantile" argument="-extract:rt_quantile" type="float" min="0.0" max="1.0" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help=""/>
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122 <param name="rt_window" argument="-extract:rt_window" type="float" min="0.0" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="If set, this parameter takes precedence over 'extract:rt_quantile'"/>
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123 </section>
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124 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
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125 <param name="peak_width" argument="-detect:peak_width" type="float" min="0.0" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
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126 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" min="0.0" value="0.2" label="Minimum elution peak width" help="Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
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127 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
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128 <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" min="0.0" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
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129 </section>
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130 <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
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131 <param name="samples" argument="-svm:samples" type="integer" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
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132 <param name="no_selection" argument="-svm:no_selection" type="boolean" truevalue="true" falsevalue="false" checked="false" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
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133 <param name="kernel" argument="-svm:kernel" type="select" label="SVM kernel" help="">
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134 <option value="RBF" selected="true">RBF</option>
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135 <option value="linear">linear</option>
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136 <expand macro="list_string_san" name="kernel"/>
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137 </param>
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138 <param name="xval" argument="-svm:xval" type="integer" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
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139 <param name="log2_C" argument="-svm:log2_C" type="text" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="A value 'x' is used as 'C = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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140 <expand macro="list_float_valsan" name="log2_C"/>
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141 </param>
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142 <param name="log2_gamma" argument="-svm:log2_gamma" type="text" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="A value 'x' is used as 'gamma = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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143 <expand macro="list_float_valsan" name="log2_gamma"/>
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144 </param>
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145 <param name="log2_p" argument="-svm:log2_p" type="text" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0" label="Values to try for the SVM parameter 'epsilon' during parameter optimization (epsilon-SVR only)" help="A value 'x' is used as 'epsilon = 2^x' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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146 <expand macro="list_float_valsan" name="log2_p"/>
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147 </param>
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148 <param name="epsilon" argument="-svm:epsilon" type="float" min="0.0" value="0.001" label="Stopping criterion" help=""/>
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149 <param name="cache_size" argument="-svm:cache_size" type="float" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
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150 <param name="no_shrinking" argument="-svm:no_shrinking" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable the shrinking heuristics" help=""/>
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151 <param name="predictors" argument="-svm:predictors" type="text" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="">
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152 <expand macro="list_string_san" name="predictors"/>
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153 </param>
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154 <param name="min_prob" argument="-svm:min_prob" type="float" min="0.0" max="1.0" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help=""/>
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155 </section>
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156 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
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157 <param name="type" argument="-model:type" type="select" label="Type of elution model to fit to features" help="">
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158 <option value="symmetric" selected="true">symmetric</option>
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159 <option value="asymmetric">asymmetric</option>
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160 <option value="none">none</option>
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161 <expand macro="list_string_san" name="type"/>
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162 </param>
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163 <param name="add_zeros" argument="-model:add_zeros" type="float" min="0.0" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="This parameter sets the weight given to these points during model fitting; '0' to disable"/>
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164 <param name="unweighted_fit" argument="-model:unweighted_fit" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help=""/>
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165 <param name="no_imputation" argument="-model:no_imputation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help=""/>
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166 <param name="each_trace" argument="-model:each_trace" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Fit elution model to each individual mass trace" help=""/>
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167 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
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168 <param name="min_area" argument="-model:check:min_area" type="float" min="0.0" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help=""/>
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169 <param name="boundaries" argument="-model:check:boundaries" type="float" min="0.0" max="1.0" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help=""/>
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170 <param name="width" argument="-model:check:width" type="float" min="0.0" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
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171 <param name="asymmetry" argument="-model:check:asymmetry" type="float" min="0.0" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores" help="'0' to disable. Not applied to individual mass traces (parameter 'each_trace')"/>
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172 </section>
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173 </section>
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174 <section name="EMGScoring" title="Parameters for fitting exp" help="mod. Gaussians to mass traces" expanded="false">
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175 <param name="max_iteration" argument="-EMGScoring:max_iteration" type="integer" min="1" value="100" label="Maximum number of iterations for EMG fitting" help=""/>
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176 <param name="init_mom" argument="-EMGScoring:init_mom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Alternative initial parameters for fitting through method of moments" help=""/>
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177 </section>
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178 <expand macro="adv_opts_macro">
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179 <param argument="-candidates_in" type="data" format="featurexml" optional="true" label="Input file: Feature candidates from a previous run" help="If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored select featurexml data sets(s)"/>
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180 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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181 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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182 <expand macro="list_string_san" name="test"/>
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183 </param>
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184 </expand>
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185 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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186 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
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187 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
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188 <option value="candidates_out_FLAG">candidates_out (Output file: Feature candidates (before filtering and model fitting))</option>
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189 <option value="xval_out_FLAG">xval_out (Output file: SVM cross-validation (parameter optimization) results)</option>
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190 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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191 </param>
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192 </inputs>
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193 <outputs>
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194 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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195 <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
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196 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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197 </data>
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198 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
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199 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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200 </data>
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201 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
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202 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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203 </data>
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204 <data name="svm_xval_out" label="${tool.name} on ${on_string}: svm:xval_out" format="csv">
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205 <filter>OPTIONAL_OUTPUTS is not None and "xval_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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206 </data>
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207 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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208 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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209 </data>
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210 </outputs>
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211 <tests>
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212 <!-- TOPP_FeatureFinderIdentification_1 -->
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213 <test expect_num_outputs="2">
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214 <section name="adv_opts">
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215 <param name="force" value="false"/>
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216 <param name="test" value="true"/>
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217 </section>
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218 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
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219 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
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220 <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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221 <param name="quantify_decoys" value="false"/>
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222 <param name="min_psm_cutoff" value="none"/>
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223 <param name="add_mass_offset_peptides" value="0.0"/>
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224 <section name="extract">
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225 <param name="batch_size" value="5000"/>
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226 <param name="mz_window" value="0.1"/>
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227 <param name="n_isotopes" value="2"/>
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228 <param name="isotope_pmin" value="0.0"/>
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229 <param name="rt_quantile" value="0.95"/>
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230 <param name="rt_window" value="0.0"/>
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231 </section>
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232 <section name="detect">
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233 <param name="peak_width" value="60.0"/>
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234 <param name="min_peak_width" value="0.2"/>
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235 <param name="signal_to_noise" value="0.8"/>
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236 <param name="mapping_tolerance" value="0.0"/>
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237 </section>
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238 <section name="svm">
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239 <param name="samples" value="0"/>
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240 <param name="no_selection" value="false"/>
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241 <param name="kernel" value="RBF"/>
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242 <param name="xval" value="5"/>
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243 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
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244 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
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245 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
15
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246 <param name="epsilon" value="0.001"/>
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247 <param name="cache_size" value="100.0"/>
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248 <param name="no_shrinking" value="false"/>
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249 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
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250 <param name="min_prob" value="0.0"/>
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251 </section>
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252 <section name="model">
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253 <param name="type" value="none"/>
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254 <param name="add_zeros" value="0.2"/>
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255 <param name="unweighted_fit" value="false"/>
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256 <param name="no_imputation" value="false"/>
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257 <param name="each_trace" value="false"/>
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258 <section name="check">
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259 <param name="min_area" value="1.0"/>
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260 <param name="boundaries" value="0.5"/>
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261 <param name="width" value="10.0"/>
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262 <param name="asymmetry" value="10.0"/>
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263 </section>
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264 </section>
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265 <section name="EMGScoring">
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266 <param name="max_iteration" value="100"/>
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267 <param name="init_mom" value="false"/>
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268 </section>
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269 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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270 <output name="ctd_out" ftype="xml">
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271 <assert_contents>
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272 <is_valid_xml/>
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273 </assert_contents>
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274 </output>
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275 <assert_stdout>
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276 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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277 </assert_stdout>
15
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278 </test>
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279 <!-- TOPP_FeatureFinderIdentification_3 -->
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280 <test expect_num_outputs="2">
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281 <section name="adv_opts">
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282 <param name="force" value="false"/>
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283 <param name="test" value="true"/>
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284 </section>
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285 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
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286 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
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287 <output name="out" value="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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288 <param name="quantify_decoys" value="false"/>
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289 <param name="min_psm_cutoff" value="none"/>
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290 <param name="add_mass_offset_peptides" value="0.0"/>
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291 <section name="extract">
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292 <param name="batch_size" value="5000"/>
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293 <param name="mz_window" value="0.1"/>
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294 <param name="n_isotopes" value="2"/>
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295 <param name="isotope_pmin" value="0.0"/>
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296 <param name="rt_quantile" value="0.95"/>
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297 <param name="rt_window" value="0.0"/>
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298 </section>
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299 <section name="detect">
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300 <param name="peak_width" value="60.0"/>
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301 <param name="min_peak_width" value="0.2"/>
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302 <param name="signal_to_noise" value="0.8"/>
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303 <param name="mapping_tolerance" value="0.0"/>
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304 </section>
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305 <section name="svm">
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306 <param name="samples" value="0"/>
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307 <param name="no_selection" value="false"/>
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308 <param name="kernel" value="RBF"/>
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309 <param name="xval" value="5"/>
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310 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
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311 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
16
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312 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
15
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313 <param name="epsilon" value="0.001"/>
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314 <param name="cache_size" value="100.0"/>
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315 <param name="no_shrinking" value="false"/>
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316 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
5dc928c83939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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317 <param name="min_prob" value="0.0"/>
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318 </section>
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319 <section name="model">
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320 <param name="type" value="symmetric"/>
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321 <param name="add_zeros" value="0.2"/>
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322 <param name="unweighted_fit" value="false"/>
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323 <param name="no_imputation" value="false"/>
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324 <param name="each_trace" value="false"/>
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325 <section name="check">
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326 <param name="min_area" value="1.0"/>
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327 <param name="boundaries" value="0.5"/>
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328 <param name="width" value="10.0"/>
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329 <param name="asymmetry" value="10.0"/>
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330 </section>
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331 </section>
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332 <section name="EMGScoring">
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333 <param name="max_iteration" value="100"/>
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334 <param name="init_mom" value="false"/>
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335 </section>
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336 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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337 <output name="ctd_out" ftype="xml">
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338 <assert_contents>
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339 <is_valid_xml/>
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340 </assert_contents>
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341 </output>
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342 <assert_stdout>
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343 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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344 </assert_stdout>
15
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345 </test>
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346 <!-- TOPP_FeatureFinderIdentification_5 -->
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347 <test expect_num_outputs="3">
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348 <section name="adv_opts">
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349 <param name="force" value="false"/>
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350 <param name="test" value="true"/>
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351 </section>
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352 <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
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353 <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
16
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354 <output name="out" value="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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355 <output name="candidates_out" value="FeatureFinderIdentification_5_candidates.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
15
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356 <param name="quantify_decoys" value="false"/>
16
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357 <param name="min_psm_cutoff" value="none"/>
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358 <param name="add_mass_offset_peptides" value="0.0"/>
15
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359 <section name="extract">
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360 <param name="batch_size" value="10"/>
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361 <param name="mz_window" value="0.1"/>
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362 <param name="n_isotopes" value="2"/>
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363 <param name="isotope_pmin" value="0.0"/>
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364 <param name="rt_quantile" value="0.95"/>
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365 <param name="rt_window" value="0.0"/>
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366 </section>
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367 <section name="detect">
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368 <param name="peak_width" value="60.0"/>
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369 <param name="min_peak_width" value="0.2"/>
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370 <param name="signal_to_noise" value="0.8"/>
5dc928c83939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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371 <param name="mapping_tolerance" value="0.0"/>
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372 </section>
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373 <section name="svm">
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374 <param name="samples" value="0"/>
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375 <param name="no_selection" value="false"/>
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376 <param name="kernel" value="RBF"/>
5dc928c83939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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377 <param name="xval" value="5"/>
5dc928c83939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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378 <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
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379 <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
16
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380 <param name="log2_p" value="-15.0 -12.0 -9.0 -6.0 -3.32192809489 0.0 3.32192809489 6.0 9.0 12.0 15.0"/>
15
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381 <param name="epsilon" value="0.001"/>
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382 <param name="cache_size" value="100.0"/>
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383 <param name="no_shrinking" value="false"/>
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384 <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_ms1_isotope_correlation_score,var_ms1_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
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385 <param name="min_prob" value="0.0"/>
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386 </section>
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387 <section name="model">
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388 <param name="type" value="none"/>
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389 <param name="add_zeros" value="0.2"/>
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390 <param name="unweighted_fit" value="false"/>
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391 <param name="no_imputation" value="false"/>
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392 <param name="each_trace" value="false"/>
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393 <section name="check">
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394 <param name="min_area" value="1.0"/>
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395 <param name="boundaries" value="0.5"/>
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396 <param name="width" value="10.0"/>
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397 <param name="asymmetry" value="10.0"/>
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398 </section>
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399 </section>
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400 <section name="EMGScoring">
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401 <param name="max_iteration" value="100"/>
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402 <param name="init_mom" value="false"/>
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403 </section>
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404 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,candidates_out_FLAG"/>
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405 <output name="ctd_out" ftype="xml">
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406 <assert_contents>
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407 <is_valid_xml/>
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408 </assert_contents>
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409 </output>
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410 <assert_stdout>
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411 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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412 </assert_stdout>
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413 </test>
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414 </tests>
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415 <help><![CDATA[Detects features in MS1 data based on peptide identifications.
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416
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417
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418 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderIdentification.html]]></help>
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419 <expand macro="references"/>
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420 </tool>