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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:13:44 +0000 |
parents | 654e2bf18e82 |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> <!--Proposed Tool Section: [Peptide property prediction]--> <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Trains a model for the retention time prediction of peptides from a training set.</description> <macros> <token name="@EXECUTABLE@">RTModel</token> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ @EXT_FOO@ #import re ## Preprocessing #if $in: mkdir in && ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if #if $in_positive: mkdir in_positive && ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' && #end if #if $in_negative: mkdir in_negative && ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' && #end if mkdir out && #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_oligo_params && #end if #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_oligo_trainset && #end if ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd #if $in: -in 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' #end if #if $in_positive: -in_positive 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' #end if #if $in_negative: -in_negative 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' #end if -out 'out/output.${gxy2omsext("txt")}' #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_oligo_params 'out_oligo_params/output.${gxy2omsext("paramxml")}' #end if #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -out_oligo_trainset 'out_oligo_trainset/output.${gxy2omsext("txt")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("txt")}' '$out' #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params' #end if #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset' #end if #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS && mv '@EXECUTABLE@.ctd' '$ctd_out' #end if]]></command> <configfiles> <inputs name="args_json" data_style="paths"/> <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> <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)"/> <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)"/> <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)"/> <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). "> <option value="NU_SVR" selected="true">NU_SVR</option> <option value="NU_SVC">NU_SVC</option> <option value="EPSILON_SVR">EPSILON_SVR</option> <option value="C_SVC">C_SVC</option> <expand macro="list_string_san" name="svm_type"/> </param> <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=""/> <param argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/> <param argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/> <param argument="-kernel_type" type="select" optional="true" label="the kernel type of the svm" help=""> <option value="LINEAR">LINEAR</option> <option value="RBF">RBF</option> <option value="POLY">POLY</option> <option value="OLIGO" selected="true">OLIGO</option> <expand macro="list_string_san" name="kernel_type"/> </param> <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=""/> <param argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/> <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=""/> <param argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/> <param argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/> <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=""/> <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=""/> <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"/> <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false"> <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=""/> <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=""/> <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/> <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/> <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/> <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/> <param name="p_start" argument="-cv:p_start" type="float" optional="true" value="1.0" label="starting point of p" help=""/> <param name="p_step_size" argument="-cv:p_step_size" type="float" optional="true" value="10.0" label="step size point of p" help=""/> <param name="p_stop" argument="-cv:p_stop" type="float" optional="true" value="1000.0" label="stopping point of p" help=""/> <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/> <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="10.0" label="step size of c" help=""/> <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/> <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=""/> <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.2" label="step size of nu" help=""/> <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=""/> <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/> <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/> <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> <expand macro="list_string_san" name="test"/> </param> </expand> <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> <option value="out_oligo_params_FLAG">out_oligo_params (output file with additional model parameters when using the OLIGO kernel)</option> <option value="out_oligo_trainset_FLAG">out_oligo_trainset (output file with the used training dataset when using the OLIGO kernel)</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/> <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml"> <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt"> <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> <tests><!-- TOPP_RTModel_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="RTModel_1_input.idXML"/> <output name="out" file="RTModel_1_output.model" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="svm_type" value="NU_SVR"/> <param name="nu" value="0.5"/> <param name="p" value="0.1"/> <param name="c" value="0.1"/> <param name="kernel_type" value="POLY"/> <param name="degree" value="1"/> <param name="border_length" value="22"/> <param name="max_std" value="10.0"/> <param name="k_mer_length" value="1"/> <param name="sigma" value="5.0"/> <param name="total_gradient_time" value="3000.0"/> <param name="first_dim_rt" value="false"/> <param name="additive_cv" value="false"/> <section name="cv"> <param name="skip_cv" value="true"/> <param name="number_of_runs" value="10"/> <param name="number_of_partitions" value="10"/> <param name="degree_start" value="1"/> <param name="degree_step_size" value="2"/> <param name="degree_stop" value="4"/> <param name="p_start" value="1.0"/> <param name="p_step_size" value="10.0"/> <param name="p_stop" value="1000.0"/> <param name="c_start" value="1.0"/> <param name="c_step_size" value="10.0"/> <param name="c_stop" value="1000.0"/> <param name="nu_start" value="0.3"/> <param name="nu_step_size" value="1.2"/> <param name="nu_stop" value="0.7"/> <param name="sigma_start" value="1.0"/> <param name="sigma_step_size" value="1.3"/> <param name="sigma_stop" value="15.0"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_RTModel_2 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in_positive" value="RTModel_2_input_positive.idXML"/> <param name="in_negative" value="RTModel_2_input_negative.idXML"/> <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="svm_type" value="NU_SVR"/> <param name="nu" value="0.5"/> <param name="p" value="0.1"/> <param name="c" value="0.5"/> <param name="kernel_type" value="OLIGO"/> <param name="degree" value="1"/> <param name="border_length" value="22"/> <param name="max_std" value="10.0"/> <param name="k_mer_length" value="1"/> <param name="sigma" value="5.0"/> <param name="total_gradient_time" value="1.0"/> <param name="first_dim_rt" value="false"/> <param name="additive_cv" value="false"/> <section name="cv"> <param name="skip_cv" value="true"/> <param name="number_of_runs" value="10"/> <param name="number_of_partitions" value="10"/> <param name="degree_start" value="1"/> <param name="degree_step_size" value="2"/> <param name="degree_stop" value="4"/> <param name="p_start" value="1.0"/> <param name="p_step_size" value="10.0"/> <param name="p_stop" value="1000.0"/> <param name="c_start" value="1.0"/> <param name="c_step_size" value="10.0"/> <param name="c_stop" value="1000.0"/> <param name="nu_start" value="0.3"/> <param name="nu_step_size" value="1.2"/> <param name="nu_stop" value="0.7"/> <param name="sigma_start" value="1.0"/> <param name="sigma_step_size" value="1.3"/> <param name="sigma_stop" value="15.0"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_RTModel_3 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="RTModel_3_input.idXML"/> <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="svm_type" value="NU_SVR"/> <param name="nu" value="0.5"/> <param name="p" value="0.1"/> <param name="c" value="0.001953125"/> <param name="kernel_type" value="OLIGO"/> <param name="degree" value="1"/> <param name="border_length" value="22"/> <param name="max_std" value="10.0"/> <param name="k_mer_length" value="1"/> <param name="sigma" value="1.0"/> <param name="total_gradient_time" value="1.0"/> <param name="first_dim_rt" value="false"/> <param name="additive_cv" value="false"/> <section name="cv"> <param name="skip_cv" value="false"/> <param name="number_of_runs" value="1"/> <param name="number_of_partitions" value="5"/> <param name="degree_start" value="1"/> <param name="degree_step_size" value="2"/> <param name="degree_stop" value="4"/> <param name="p_start" value="1.0"/> <param name="p_step_size" value="10.0"/> <param name="p_stop" value="1000.0"/> <param name="c_start" value="0.001953125"/> <param name="c_step_size" value="2.0"/> <param name="c_stop" value="0.001953125"/> <param name="nu_start" value="0.4"/> <param name="nu_step_size" value="1.2"/> <param name="nu_stop" value="0.4"/> <param name="sigma_start" value="5.0"/> <param name="sigma_step_size" value="1.221055"/> <param name="sigma_stop" value="5.0"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> <!-- TOPP_RTModel_4 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="RTModel_4_input.txt" ftype="txt"/> <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="txt"/> <param name="svm_type" value="NU_SVR"/> <param name="nu" value="0.5"/> <param name="p" value="0.1"/> <param name="c" value="0.001953125"/> <param name="kernel_type" value="OLIGO"/> <param name="degree" value="1"/> <param name="border_length" value="22"/> <param name="max_std" value="10.0"/> <param name="k_mer_length" value="1"/> <param name="sigma" value="1.0"/> <param name="total_gradient_time" value="1.0"/> <param name="first_dim_rt" value="false"/> <param name="additive_cv" value="false"/> <section name="cv"> <param name="skip_cv" value="false"/> <param name="number_of_runs" value="1"/> <param name="number_of_partitions" value="5"/> <param name="degree_start" value="1"/> <param name="degree_step_size" value="2"/> <param name="degree_stop" value="4"/> <param name="p_start" value="1.0"/> <param name="p_step_size" value="10.0"/> <param name="p_stop" value="1000.0"/> <param name="c_start" value="0.001953125"/> <param name="c_step_size" value="2.0"/> <param name="c_stop" value="0.001953125"/> <param name="nu_start" value="0.4"/> <param name="nu_step_size" value="1.2"/> <param name="nu_stop" value="0.4"/> <param name="sigma_start" value="5.0"/> <param name="sigma_step_size" value="1.221055"/> <param name="sigma_stop" value="5.0"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> </test> </tests> <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set. For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_RTModel.html]]></help> <expand macro="references"/> </tool>