Mercurial > repos > galaxyp > openms_featurefinderidentification

annotate FeatureFinderIdentification.xml @ 14:17ecb923aa31 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 20:22:43 +0000
parents 5471eba33b70
children 5dc928c83939
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3a61c78033f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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="FeatureFinderIdentification" name="FeatureFinderIdentification" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Detects features in MS1 data based on peptide identifications.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderIdentification</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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3a61c78033f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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($in.ext)' &&
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21 mkdir id &&
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22 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
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23 #if $id_ext:
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24 mkdir id_ext &&
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25 ln -s '$id_ext' 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)' &&
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26 #end if
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27 mkdir out &&
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28 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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29 mkdir lib_out &&
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3a61c78033f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 #end if
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31 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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32 mkdir chrom_out &&
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33 #end if
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34 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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35 mkdir candidates_out &&
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36 #end if
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37 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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38 mkdir svm_xval_out &&
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39 #end if
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40 #if $adv_opts_cond.adv_opts_selector=='advanced':
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41 #if $adv_opts_cond.candidates_in:
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42 mkdir adv_opts_cond.candidates_in &&
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43 ln -s '$adv_opts_cond.candidates_in' 'adv_opts_cond.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts_cond.candidates_in.element_identifier)}.$gxy2omsext($adv_opts_cond.candidates_in.ext)' &&
3
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44 #end if
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45 #end if
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46
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47 ## Main program call
3
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48
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49 set -o pipefail &&
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50 @EXECUTABLE@ -write_ctd ./ &&
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51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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53 -in
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54 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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55 -id
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56 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
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57 #if $id_ext:
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58 -id_ext
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59 'id_ext/${re.sub("[^\w\-_]", "_", $id_ext.element_identifier)}.$gxy2omsext($id_ext.ext)'
3
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60 #end if
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61 -out
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62 'out/output.${gxy2omsext("featurexml")}'
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63 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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64 -lib_out
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65 'lib_out/output.${gxy2omsext("traml")}'
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66 #end if
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67 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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68 -chrom_out
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69 'chrom_out/output.${gxy2omsext("mzml")}'
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70 #end if
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71 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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72 -candidates_out
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73 'candidates_out/output.${gxy2omsext("featurexml")}'
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74 #end if
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75 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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76 -svm:xval_out
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77 'svm_xval_out/output.${gxy2omsext("csv")}'
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78 #end if
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79 #if $adv_opts_cond.adv_opts_selector=='advanced':
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80 #if $adv_opts_cond.candidates_in:
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81 -candidates_in
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82 'adv_opts_cond.candidates_in/${re.sub("[^\w\-_]", "_", $adv_opts_cond.candidates_in.element_identifier)}.$gxy2omsext($adv_opts_cond.candidates_in.ext)'
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83 #end if
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84 #end if
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85 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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86 | tee '$stdout'
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87 #end if
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88
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89 ## Postprocessing
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90 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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91 #if "lib_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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92 && mv 'lib_out/output.${gxy2omsext("traml")}' '$lib_out'
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93 #end if
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94 #if "chrom_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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95 && mv 'chrom_out/output.${gxy2omsext("mzml")}' '$chrom_out'
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96 #end if
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97 #if "candidates_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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98 && mv 'candidates_out/output.${gxy2omsext("featurexml")}' '$candidates_out'
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99 #end if
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100 #if "xval_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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101 && mv 'svm_xval_out/output.${gxy2omsext("csv")}' '$svm_xval_out'
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102 #end if
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103 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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104 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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105 #end if]]></command>
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106 <configfiles>
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107 <inputs name="args_json" data_style="paths"/>
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108 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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109 </configfiles>
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110 <inputs>
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111 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: LC-MS raw data" help=" select mzml data sets(s)"/>
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112 <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Input file: Peptide identifications derived directly from 'in'" help=" select idxml data sets(s)"/>
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113 <param name="id_ext" 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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114 <section name="extract" title="Parameters for ion chromatogram extraction" help="" expanded="false">
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115 <param name="batch_size" argument="-extract:batch_size" type="integer" optional="true" min="1" value="1000" label="Nr of peptides used in each batch of chromatogram extraction" help="Smaller values decrease memory usage but increase runtime"/>
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116 <param name="mz_window" argument="-extract:mz_window" type="float" optional="true" 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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117 <param name="n_isotopes" argument="-extract:n_isotopes" type="integer" optional="true" min="2" value="2" label="Number of isotopes to include in each peptide assay" help=""/>
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118 <param name="isotope_pmin" argument="-extract:isotope_pmin" type="float" optional="true" 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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119 <param name="rt_quantile" argument="-extract:rt_quantile" type="float" optional="true" 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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120 <param name="rt_window" argument="-extract:rt_window" type="float" optional="true" 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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121 </section>
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122 <section name="detect" title="Parameters for detecting features in extracted ion chromatograms" help="" expanded="false">
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123 <param name="peak_width" argument="-detect:peak_width" type="float" optional="true" 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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124 <param name="min_peak_width" argument="-detect:min_peak_width" type="float" optional="true" 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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125 <param name="signal_to_noise" argument="-detect:signal_to_noise" type="float" optional="true" min="0.1" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help=""/>
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126 <param name="mapping_tolerance" argument="-detect:mapping_tolerance" type="float" optional="true" 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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127 </section>
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128 <section name="svm" title="Parameters for scoring features using a support vector machine (SVM)" help="" expanded="false">
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129 <param name="samples" argument="-svm:samples" type="integer" optional="true" min="0" value="0" label="Number of observations to use for training ('0' for all)" help=""/>
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130 <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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131 <param name="kernel" argument="-svm:kernel" display="radio" type="select" optional="false" label="SVM kernel" help="">
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132 <option value="RBF" selected="true">RBF</option>
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133 <option value="linear">linear</option>
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134 <expand macro="list_string_san"/>
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135 </param>
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136 <param name="xval" argument="-svm:xval" type="integer" optional="true" min="1" value="5" label="Number of partitions for cross-validation (parameter optimization)" help=""/>
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137 <param name="log2_C" argument="-svm:log2_C" type="text" optional="true" 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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138 <expand macro="list_float_valsan"/>
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139 </param>
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140 <param name="log2_gamma" argument="-svm:log2_gamma" type="text" optional="true" 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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141 <expand macro="list_float_valsan"/>
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142 </param>
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143 <param name="epsilon" argument="-svm:epsilon" type="float" optional="true" min="0.0" value="0.001" label="Stopping criterion" help=""/>
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144 <param name="cache_size" argument="-svm:cache_size" type="float" optional="true" min="1.0" value="100.0" label="Size of the kernel cache (in MB)" help=""/>
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145 <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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146 <param name="predictors" argument="-svm:predictors" type="text" optional="true" 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_isotope_correlation_score,var_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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147 <expand macro="list_string_san"/>
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148 </param>
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149 <param name="min_prob" argument="-svm:min_prob" type="float" optional="true" 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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150 </section>
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151 <section name="model" title="Parameters for fitting elution models to features" help="" expanded="false">
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152 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of elution model to fit to features" help="">
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153 <option value="symmetric" selected="true">symmetric</option>
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154 <option value="asymmetric">asymmetric</option>
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155 <option value="none">none</option>
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156 <expand macro="list_string_san"/>
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157 </param>
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158 <param name="add_zeros" argument="-model:add_zeros" type="float" optional="true" 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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159 <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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160 <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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161 <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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162 <section name="check" title="Parameters for checking the validity of elution models (and rejecting them if necessary)" help="" expanded="false">
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163 <param name="min_area" argument="-model:check:min_area" type="float" optional="true" 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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164 <param name="boundaries" argument="-model:check:boundaries" type="float" optional="true" 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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165 <param name="width" argument="-model:check:width" type="float" optional="true" 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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166 <param name="asymmetry" argument="-model:check:asymmetry" type="float" optional="true" 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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167 </section>
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168 </section>
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169 <expand macro="adv_opts_macro">
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170 <param name="candidates_in" 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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171 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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172 <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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173 <expand macro="list_string_san"/>
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174 </param>
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175 </expand>
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176 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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177 <option value="lib_out_FLAG">lib_out (Output file: Assay library)</option>
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178 <option value="chrom_out_FLAG">chrom_out (Output file: Chromatograms)</option>
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179 <option value="candidates_out_FLAG">candidates_out (Output file: Feature candidates (before filtering and model fitting))</option>
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180 <option value="xval_out_FLAG">xval_out (Output file: SVM cross-validation (parameter optimization) results)</option>
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181 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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182 </param>
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183 </inputs>
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184 <outputs>
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185 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
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186 <data name="lib_out" label="${tool.name} on ${on_string}: lib_out" format="traml">
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187 <filter>OPTIONAL_OUTPUTS is not None and "lib_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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188 </data>
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189 <data name="chrom_out" label="${tool.name} on ${on_string}: chrom_out" format="mzml">
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190 <filter>OPTIONAL_OUTPUTS is not None and "chrom_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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191 </data>
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192 <data name="candidates_out" label="${tool.name} on ${on_string}: candidates_out" format="featurexml">
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193 <filter>OPTIONAL_OUTPUTS is not None and "candidates_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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194 </data>
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195 <data name="svm_xval_out" label="${tool.name} on ${on_string}: svm:xval_out" format="csv">
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196 <filter>OPTIONAL_OUTPUTS is not None and "xval_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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197 </data>
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198 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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199 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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200 </data>
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201 </outputs>
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202 <tests>
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203 <expand macro="autotest_FeatureFinderIdentification"/>
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204 <expand macro="manutest_FeatureFinderIdentification"/>
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205 </tests>
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206 <help><![CDATA[Detects features in MS1 data based on peptide identifications.
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207
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208
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209 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderIdentification.html]]></help>
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210 <expand macro="references"/>
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211 </tool>