Mercurial > repos > galaxyp > openms_ptmodel

annotate PTModel.xml @ 11:6c281fbfefff 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 20:17:18 +0000
parents b6db68398c9e
children 3e9d04994968
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2b34b435c177 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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a174f62788b7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: [Peptide property prediction]-->
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4 <tool id="PTModel" name="PTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PTModel</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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2b34b435c177 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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11 </macros>
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12 <expand macro="requirements"/>
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2b34b435c177 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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039029f54c89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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18 ## Preprocessing
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19 mkdir in_positive &&
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20 ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
039029f54c89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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21 mkdir in_negative &&
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22 ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
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23 mkdir out &&
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24 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
b6db68398c9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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25 mkdir out_oligo_params &&
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26 #end if
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27 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
b6db68398c9e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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28 mkdir out_oligo_trainset &&
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29 #end if
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039029f54c89 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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31 ## Main program call
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2b34b435c177 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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32
8
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33 set -o pipefail &&
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34 @EXECUTABLE@ -write_ctd ./ &&
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35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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37 -in_positive
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38 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
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39 -in_negative
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40 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
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41 -out
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42 'out/output.${gxy2omsext("txt")}'
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43 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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44 -out_oligo_params
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45 'out_oligo_params/output.${gxy2omsext("paramxml")}'
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46 #end if
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47 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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48 -out_oligo_trainset
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49 'out_oligo_trainset/output.${gxy2omsext("txt")}'
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50 #end if
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51 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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52 | tee '$stdout'
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53 #end if
8
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54
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55 ## Postprocessing
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56 && mv 'out/output.${gxy2omsext("txt")}' '$out'
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57 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
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59 #end if
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60 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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61 && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
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62 #end if
8
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63 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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64 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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65 #end if]]></command>
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66 <configfiles>
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67 <inputs name="args_json" data_style="paths"/>
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68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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69 </configfiles>
0
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70 <inputs>
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71 <param name="in_positive" argument="-in_positive" type="data" format="idxml" optional="false" label="input file with positive examples" help=" select idxml data sets(s)"/>
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72 <param name="in_negative" argument="-in_negative" type="data" format="idxml" optional="false" label="input file with negative examples" help=" select idxml data sets(s)"/>
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73 <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
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74 <param name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" label="the type of the svm (NU_SVC or C_SVC)" help="">
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75 <option value="NU_SVC">NU_SVC</option>
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76 <option value="C_SVC" selected="true">C_SVC</option>
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77 <expand macro="list_string_san"/>
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78 </param>
8
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79 <param name="nu" argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
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80 <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" label="the kernel type of the svm" help="">
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81 <option value="LINEAR">LINEAR</option>
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82 <option value="RBF">RBF</option>
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83 <option value="POLY">POLY</option>
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84 <option value="OLIGO" selected="true">OLIGO</option>
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85 <expand macro="list_string_san"/>
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86 </param>
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87 <param name="degree" argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
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88 <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
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89 <param name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
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90 <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
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91 <param name="max_positive_count" argument="-max_positive_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
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92 <param name="max_negative_count" argument="-max_negative_count" type="integer" optional="true" min="1" value="1000" label="quantity of positive samples for training (randomly chosen if smaller than available quantity)" help=""/>
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93 <param name="redundant" argument="-redundant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the input sets are redundant and the redundant peptides should occur more than once in the training set, this flag has to be set" help=""/>
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94 <param name="additive_cv" argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied with the step size to get the new value" help=""/>
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95 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
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96 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Has to be set if the cv should be skipped and the model should just be trained with the specified parameters" help=""/>
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97 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="10" label="number of runs for the CV" help=""/>
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98 <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
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99 <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
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100 <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
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101 <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
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102 <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
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103 <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="100.0" label="step size of c" help=""/>
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104 <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
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105 <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="starting point of nu" help=""/>
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106 <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.3" label="step size of nu" help=""/>
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107 <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.9" label="stopping point of nu" help=""/>
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108 <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
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109 <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
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110 <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
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111 </section>
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112 <expand macro="adv_opts_macro">
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113 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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114 <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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115 <expand macro="list_string_san"/>
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116 </param>
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117 </expand>
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118 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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119 <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option>
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120 <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option>
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121 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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122 </param>
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123 </inputs>
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124 <outputs>
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125 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
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126 <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
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127 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
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128 </data>
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129 <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
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130 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
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131 </data>
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132 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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133 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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134 </data>
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135 </outputs>
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136 <tests>
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137 <expand macro="autotest_PTModel"/>
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138 <expand macro="manutest_PTModel"/>
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139 </tests>
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140 <help><![CDATA[Trains a model for the prediction of proteotypic peptides from a training set.
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141
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142
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143 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PTModel.html]]></help>
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144 <expand macro="references"/>
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145 </tool>