Mercurial > repos > galaxyp > openms_featurefinderidentification

annotate FeatureFinderIdentification.xml @ 1:6a3bbd5b8cb6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 16:04:04 -0400
parents 3a61c78033f0
children c040ffc3ac9b
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.1.0">
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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 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FeatureFinderIdentification
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_id:
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19 -id $param_id
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_lib_out:
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25 -lib_out $param_lib_out
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26 #end if
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27 #if $param_chrom_out:
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28 -chrom_out $param_chrom_out
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29 #end if
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30 #if $param_trafo_out:
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31 -trafo_out $param_trafo_out
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32 #end if
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33 #if $param_extract_reference_rt:
1
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34 -extract:reference_rt
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35 #if " " in str($param_extract_reference_rt):
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36 "$param_extract_reference_rt"
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37 #else
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38 $param_extract_reference_rt
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39 #end if
0
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40 #end if
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41 #if $param_extract_rt_window:
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42 -extract:rt_window $param_extract_rt_window
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43 #end if
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44 #if $param_extract_mz_window:
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45 -extract:mz_window $param_extract_mz_window
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46 #end if
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47 #if $param_extract_isotope_pmin:
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48 -extract:isotope_pmin $param_extract_isotope_pmin
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49 #end if
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50 #if $param_detect_peak_width:
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51 -detect:peak_width $param_detect_peak_width
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52 #end if
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53 #if $param_model_type:
1
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54 -model:type
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55 #if " " in str($param_model_type):
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56 "$param_model_type"
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57 #else
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58 $param_model_type
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59 #end if
0
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60 #end if
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61 #if $adv_opts.adv_opts_selector=='advanced':
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62 #if $adv_opts.param_force:
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63 -force
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64 #end if
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65 #if $adv_opts.param_detect_all_features:
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66 -detect:all_features
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67 #end if
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68 #if $adv_opts.param_model_add_zeros:
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69 -model:add_zeros $adv_opts.param_model_add_zeros
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70 #end if
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71 #if $adv_opts.param_model_unweighted_fit:
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72 -model:unweighted_fit
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73 #end if
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74 #if $adv_opts.param_model_no_imputation:
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75 -model:no_imputation
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76 #end if
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77 #if $adv_opts.param_model_check_boundaries:
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78 -model:check:boundaries $adv_opts.param_model_check_boundaries
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79 #end if
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80 #if $adv_opts.param_model_check_width:
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81 -model:check:width $adv_opts.param_model_check_width
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82 #end if
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83 #if $adv_opts.param_model_check_asymmetry:
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84 -model:check:asymmetry $adv_opts.param_model_check_asymmetry
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85 #end if
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86 #end if
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87 </command>
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88 <inputs>
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89 <param name="param_in" type="data" format="mzml" optional="False" label="Input file (LC-MS raw data)" help="(-in) "/>
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90 <param name="param_id" type="data" format="idxml" optional="False" label="Input file (peptide identifications)" help="(-id) "/>
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91 <param name="param_extract_reference_rt" type="select" optional="False" value="adapt" label="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge" help="(-reference_rt) 'adapt': adapt (extend) RT windows based on IDs; 'score': RT of the best-scoring ID; 'intensity': RT of the ID with the most intense precursor; 'median': median RT of all IDs; 'all': no single reference, use RTs of all IDs (requires further processing of results)">
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92 <option value="adapt" selected="true">adapt</option>
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93 <option value="score">score</option>
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94 <option value="intensity">intensity</option>
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95 <option value="median">median</option>
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96 <option value="all">all</option>
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97 </param>
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98 <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="60.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) "/>
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99 <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
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100 <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.03" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) "/>
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101 <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="30.0" label="Elution peak width in seconds for smoothing (Gauss filter)" help="(-peak_width) "/>
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102 <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
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103 <option value="symmetric" selected="true">symmetric</option>
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104 <option value="asymmetric">asymmetric</option>
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105 <option value="none">none</option>
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106 </param>
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107 <expand macro="advanced_options">
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108 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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109 <param name="param_detect_all_features" display="radio" type="boolean" truevalue="-detect:all_features" falsevalue="" checked="false" optional="True" label="Return all features detected by OpenSWATH for an assay, instead of only the best one" help="(-all_features) (This requires further processing of the results.)"/>
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110 <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
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111 <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
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112 <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" 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="(-no_imputation) "/>
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113 <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" 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="(-boundaries) "/>
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114 <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
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115 <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
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116 </expand>
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117 </inputs>
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118 <outputs>
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119 <data name="param_out" format="featurexml"/>
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120 <data name="param_lib_out" format="traml"/>
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121 <data name="param_chrom_out" format="mzml"/>
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122 <data name="param_trafo_out" format="trafoxml"/>
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123 </outputs>
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124 <help>Detects features in MS1 data based on peptide identifications.
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125
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126
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127 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help>
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128 </tool>