annotate RTModel.xml @ 12:0fc4aa40badb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:13:44 +0000
parents 654e2bf18e82
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8480765683cf 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: [Peptide property prediction]-->
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4 <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RTModel</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 #if $in:
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18 mkdir in &&
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19 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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20 #end if
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21 #if $in_positive:
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22 mkdir in_positive &&
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23 ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
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24 #end if
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25 #if $in_negative:
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26 mkdir in_negative &&
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27 ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
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28 #end if
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29 mkdir out &&
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30 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir out_oligo_params &&
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32 #end if
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33 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir out_oligo_trainset &&
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35 #end if
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36
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37 ## Main program call
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38
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 #if $in:
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44 -in
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45 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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46 #end if
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47 #if $in_positive:
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48 -in_positive
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49 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
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50 #end if
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51 #if $in_negative:
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52 -in_negative
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53 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
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54 #end if
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55 -out
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56 'out/output.${gxy2omsext("txt")}'
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57 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 -out_oligo_params
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59 'out_oligo_params/output.${gxy2omsext("paramxml")}'
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60 #end if
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61 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 -out_oligo_trainset
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63 'out_oligo_trainset/output.${gxy2omsext("txt")}'
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64 #end if
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65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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66 | tee '$stdout'
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67 #end if
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68
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69 ## Postprocessing
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70 && mv 'out/output.${gxy2omsext("txt")}' '$out'
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71 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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72 && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
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73 #end if
8
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74 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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75 && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
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76 #end if
8
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77 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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78 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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79 #end if]]></command>
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80 <configfiles>
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81 <inputs name="args_json" data_style="paths"/>
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82 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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83 </configfiles>
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84 <inputs>
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85 <param argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.. select idxml,txt data sets(s)"/>
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86 <param argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
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87 <param argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
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88 <param argument="-svm_type" type="select" optional="true" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). ">
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89 <option value="NU_SVR" selected="true">NU_SVR</option>
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90 <option value="NU_SVC">NU_SVC</option>
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91 <option value="EPSILON_SVR">EPSILON_SVR</option>
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92 <option value="C_SVC">C_SVC</option>
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93 <expand macro="list_string_san" name="svm_type"/>
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94 </param>
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95 <param 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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96 <param argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/>
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97 <param argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
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98 <param argument="-kernel_type" type="select" optional="true" label="the kernel type of the svm" help="">
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99 <option value="LINEAR">LINEAR</option>
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100 <option value="RBF">RBF</option>
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101 <option value="POLY">POLY</option>
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102 <option value="OLIGO" selected="true">OLIGO</option>
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103 <expand macro="list_string_san" name="kernel_type"/>
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104 </param>
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105 <param 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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106 <param argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
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107 <param argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/>
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108 <param argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
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109 <param argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
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110 <param argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/>
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111 <param argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/>
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112 <param 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" help="with the step size to get the new value"/>
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113 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
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114 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/>
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115 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/>
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116 <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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117 <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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118 <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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119 <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
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120 <param name="p_start" argument="-cv:p_start" type="float" optional="true" value="1.0" label="starting point of p" help=""/>
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121 <param name="p_step_size" argument="-cv:p_step_size" type="float" optional="true" value="10.0" label="step size point of p" help=""/>
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122 <param name="p_stop" argument="-cv:p_stop" type="float" optional="true" value="1000.0" label="stopping point of p" help=""/>
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123 <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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124 <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="10.0" label="step size of c" help=""/>
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125 <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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126 <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
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127 <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.2" label="step size of nu" help=""/>
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128 <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="stopping point of nu" help=""/>
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129 <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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130 <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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131 <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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132 </section>
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133 <expand macro="adv_opts_macro">
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134 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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135 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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136 <expand macro="list_string_san" name="test"/>
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137 </param>
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138 </expand>
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139 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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140 <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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141 <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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142 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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143 </param>
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144 </inputs>
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145 <outputs>
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146 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
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147 <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
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148 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
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149 </data>
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150 <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
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151 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
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152 </data>
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153 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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154 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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155 </data>
0
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156 </outputs>
12
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157 <tests><!-- TOPP_RTModel_1 -->
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158 <test expect_num_outputs="2">
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159 <section name="adv_opts">
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160 <param name="force" value="false"/>
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161 <param name="test" value="true"/>
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162 </section>
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163 <param name="in" value="RTModel_1_input.idXML"/>
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164 <output name="out" file="RTModel_1_output.model" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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165 <param name="svm_type" value="NU_SVR"/>
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166 <param name="nu" value="0.5"/>
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167 <param name="p" value="0.1"/>
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168 <param name="c" value="0.1"/>
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169 <param name="kernel_type" value="POLY"/>
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170 <param name="degree" value="1"/>
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171 <param name="border_length" value="22"/>
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172 <param name="max_std" value="10.0"/>
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173 <param name="k_mer_length" value="1"/>
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174 <param name="sigma" value="5.0"/>
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175 <param name="total_gradient_time" value="3000.0"/>
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176 <param name="first_dim_rt" value="false"/>
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177 <param name="additive_cv" value="false"/>
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178 <section name="cv">
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179 <param name="skip_cv" value="true"/>
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180 <param name="number_of_runs" value="10"/>
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181 <param name="number_of_partitions" value="10"/>
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182 <param name="degree_start" value="1"/>
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183 <param name="degree_step_size" value="2"/>
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184 <param name="degree_stop" value="4"/>
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185 <param name="p_start" value="1.0"/>
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186 <param name="p_step_size" value="10.0"/>
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187 <param name="p_stop" value="1000.0"/>
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188 <param name="c_start" value="1.0"/>
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189 <param name="c_step_size" value="10.0"/>
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190 <param name="c_stop" value="1000.0"/>
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191 <param name="nu_start" value="0.3"/>
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192 <param name="nu_step_size" value="1.2"/>
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193 <param name="nu_stop" value="0.7"/>
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194 <param name="sigma_start" value="1.0"/>
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195 <param name="sigma_step_size" value="1.3"/>
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196 <param name="sigma_stop" value="15.0"/>
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197 </section>
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198 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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199 <output name="ctd_out" ftype="xml">
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200 <assert_contents>
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201 <is_valid_xml/>
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202 </assert_contents>
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203 </output>
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204 </test>
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205 <!-- TOPP_RTModel_2 -->
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206 <test expect_num_outputs="2">
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207 <section name="adv_opts">
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208 <param name="force" value="false"/>
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209 <param name="test" value="true"/>
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210 </section>
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211 <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
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212 <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
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213 <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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214 <param name="svm_type" value="NU_SVR"/>
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215 <param name="nu" value="0.5"/>
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216 <param name="p" value="0.1"/>
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217 <param name="c" value="0.5"/>
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218 <param name="kernel_type" value="OLIGO"/>
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219 <param name="degree" value="1"/>
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220 <param name="border_length" value="22"/>
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221 <param name="max_std" value="10.0"/>
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222 <param name="k_mer_length" value="1"/>
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223 <param name="sigma" value="5.0"/>
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224 <param name="total_gradient_time" value="1.0"/>
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225 <param name="first_dim_rt" value="false"/>
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226 <param name="additive_cv" value="false"/>
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227 <section name="cv">
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228 <param name="skip_cv" value="true"/>
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229 <param name="number_of_runs" value="10"/>
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230 <param name="number_of_partitions" value="10"/>
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231 <param name="degree_start" value="1"/>
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232 <param name="degree_step_size" value="2"/>
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233 <param name="degree_stop" value="4"/>
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234 <param name="p_start" value="1.0"/>
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235 <param name="p_step_size" value="10.0"/>
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236 <param name="p_stop" value="1000.0"/>
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237 <param name="c_start" value="1.0"/>
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238 <param name="c_step_size" value="10.0"/>
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239 <param name="c_stop" value="1000.0"/>
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240 <param name="nu_start" value="0.3"/>
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241 <param name="nu_step_size" value="1.2"/>
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242 <param name="nu_stop" value="0.7"/>
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243 <param name="sigma_start" value="1.0"/>
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244 <param name="sigma_step_size" value="1.3"/>
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245 <param name="sigma_stop" value="15.0"/>
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246 </section>
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247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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248 <output name="ctd_out" ftype="xml">
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249 <assert_contents>
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250 <is_valid_xml/>
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251 </assert_contents>
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252 </output>
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253 </test>
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254 <!-- TOPP_RTModel_3 -->
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255 <test expect_num_outputs="2">
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256 <section name="adv_opts">
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257 <param name="force" value="false"/>
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258 <param name="test" value="true"/>
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259 </section>
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260 <param name="in" value="RTModel_3_input.idXML"/>
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261 <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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262 <param name="svm_type" value="NU_SVR"/>
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263 <param name="nu" value="0.5"/>
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264 <param name="p" value="0.1"/>
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265 <param name="c" value="0.001953125"/>
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266 <param name="kernel_type" value="OLIGO"/>
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267 <param name="degree" value="1"/>
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268 <param name="border_length" value="22"/>
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269 <param name="max_std" value="10.0"/>
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270 <param name="k_mer_length" value="1"/>
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271 <param name="sigma" value="1.0"/>
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272 <param name="total_gradient_time" value="1.0"/>
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273 <param name="first_dim_rt" value="false"/>
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274 <param name="additive_cv" value="false"/>
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275 <section name="cv">
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276 <param name="skip_cv" value="false"/>
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277 <param name="number_of_runs" value="1"/>
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278 <param name="number_of_partitions" value="5"/>
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279 <param name="degree_start" value="1"/>
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280 <param name="degree_step_size" value="2"/>
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281 <param name="degree_stop" value="4"/>
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282 <param name="p_start" value="1.0"/>
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283 <param name="p_step_size" value="10.0"/>
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284 <param name="p_stop" value="1000.0"/>
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285 <param name="c_start" value="0.001953125"/>
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286 <param name="c_step_size" value="2.0"/>
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287 <param name="c_stop" value="0.001953125"/>
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288 <param name="nu_start" value="0.4"/>
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289 <param name="nu_step_size" value="1.2"/>
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290 <param name="nu_stop" value="0.4"/>
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291 <param name="sigma_start" value="5.0"/>
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292 <param name="sigma_step_size" value="1.221055"/>
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293 <param name="sigma_stop" value="5.0"/>
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294 </section>
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295 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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296 <output name="ctd_out" ftype="xml">
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297 <assert_contents>
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298 <is_valid_xml/>
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299 </assert_contents>
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300 </output>
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301 </test>
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302 <!-- TOPP_RTModel_4 -->
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303 <test expect_num_outputs="2">
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304 <section name="adv_opts">
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305 <param name="force" value="false"/>
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306 <param name="test" value="true"/>
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307 </section>
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308 <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
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309 <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/>
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310 <param name="svm_type" value="NU_SVR"/>
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311 <param name="nu" value="0.5"/>
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312 <param name="p" value="0.1"/>
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313 <param name="c" value="0.001953125"/>
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314 <param name="kernel_type" value="OLIGO"/>
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315 <param name="degree" value="1"/>
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316 <param name="border_length" value="22"/>
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317 <param name="max_std" value="10.0"/>
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318 <param name="k_mer_length" value="1"/>
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319 <param name="sigma" value="1.0"/>
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320 <param name="total_gradient_time" value="1.0"/>
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321 <param name="first_dim_rt" value="false"/>
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322 <param name="additive_cv" value="false"/>
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323 <section name="cv">
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324 <param name="skip_cv" value="false"/>
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325 <param name="number_of_runs" value="1"/>
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326 <param name="number_of_partitions" value="5"/>
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327 <param name="degree_start" value="1"/>
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328 <param name="degree_step_size" value="2"/>
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329 <param name="degree_stop" value="4"/>
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330 <param name="p_start" value="1.0"/>
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331 <param name="p_step_size" value="10.0"/>
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332 <param name="p_stop" value="1000.0"/>
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333 <param name="c_start" value="0.001953125"/>
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334 <param name="c_step_size" value="2.0"/>
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335 <param name="c_stop" value="0.001953125"/>
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336 <param name="nu_start" value="0.4"/>
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337 <param name="nu_step_size" value="1.2"/>
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338 <param name="nu_stop" value="0.4"/>
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339 <param name="sigma_start" value="5.0"/>
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340 <param name="sigma_step_size" value="1.221055"/>
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341 <param name="sigma_stop" value="5.0"/>
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342 </section>
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343 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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344 <output name="ctd_out" ftype="xml">
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345 <assert_contents>
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346 <is_valid_xml/>
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347 </assert_contents>
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348 </output>
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349 </test>
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350 </tests>
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351 <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set.
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352
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353
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354 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_RTModel.html]]></help>
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355 <expand macro="references"/>
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356 </tool>