Mercurial > repos > galaxyp > openms_rtmodel
diff RTModel.xml @ 8:a9ece00a3e54 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:07:56 +0000 |
| parents | 6d4530bc334c |
| children | 654e2bf18e82 |
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--- a/RTModel.xml Fri May 17 10:25:59 2019 -0400 +++ b/RTModel.xml Wed Sep 09 20:07:56 2020 +0000 @@ -1,200 +1,168 @@ <?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="2.3.0"> +<tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <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> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[RTModel + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re -#if $param_in: - -in $param_in -#end if -#if $param_in_positive: - -in_positive $param_in_positive -#end if -#if $param_in_negative: - -in_negative $param_in_negative +## Preprocessing +#if $in: + mkdir in && + ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && #end if -#if $param_out: - -out $param_out -#end if -#if $param_out_oligo_params: - -out_oligo_params $param_out_oligo_params -#end if -#if $param_out_oligo_trainset: - -out_oligo_trainset $param_out_oligo_trainset -#end if -#if $param_svm_type: - -svm_type - #if " " in str($param_svm_type): - "$param_svm_type" - #else - $param_svm_type - #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 $param_nu: - -nu $param_nu -#end if -#if $param_p: - -p $param_p +#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 -#if $param_c: - -c $param_c +mkdir out && +#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_oligo_params && #end if -#if $param_kernel_type: - -kernel_type - #if " " in str($param_kernel_type): - "$param_kernel_type" - #else - $param_kernel_type - #end if +#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + mkdir out_oligo_trainset && #end if -#if $param_degree: - -degree $param_degree -#end if -#if $param_border_length: - -border_length $param_border_length -#end if -#if $param_max_std: - -max_std $param_max_std -#end if -#if $param_k_mer_length: - -k_mer_length $param_k_mer_length -#end if -#if $param_sigma: - -sigma $param_sigma -#end if -#if $param_total_gradient_time: - -total_gradient_time $param_total_gradient_time + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__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 $param_first_dim_rt: - -first_dim_rt -#end if -#if $param_additive_cv: - -additive_cv -#end if -#if $param_cv_skip_cv: - -cv:skip_cv +#if $in_positive: + -in_positive + 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' #end if -#if $param_cv_number_of_runs: - -cv:number_of_runs $param_cv_number_of_runs -#end if -#if $param_cv_number_of_partitions: - -cv:number_of_partitions $param_cv_number_of_partitions -#end if -#if $param_cv_degree_start: - -cv:degree_start $param_cv_degree_start +#if $in_negative: + -in_negative + 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' #end if -#if $param_cv_degree_step_size: - -cv:degree_step_size $param_cv_degree_step_size -#end if -#if $param_cv_degree_stop: - -cv:degree_stop $param_cv_degree_stop -#end if -#if $param_cv_p_start: - -cv:p_start $param_cv_p_start +-out +'out/output.${gxy2omsext("txt")}' +#if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_oligo_params + 'out_oligo_params/output.${gxy2omsext("paramxml")}' #end if -#if $param_cv_p_step_size: - -cv:p_step_size $param_cv_p_step_size +#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + -out_oligo_trainset + 'out_oligo_trainset/output.${gxy2omsext("txt")}' #end if -#if $param_cv_p_stop: - -cv:p_stop $param_cv_p_stop -#end if -#if $param_cv_c_start: - -cv:c_start $param_cv_c_start +#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 + | tee '$stdout' #end if -#if $param_cv_c_step_size: - -cv:c_step_size $param_cv_c_step_size -#end if -#if $param_cv_c_stop: - -cv:c_stop $param_cv_c_stop -#end if -#if $param_cv_nu_start: - -cv:nu_start $param_cv_nu_start + +## Postprocessing +&& mv 'out/output.${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 $param_cv_nu_step_size: - -cv:nu_step_size $param_cv_nu_step_size -#end if -#if $param_cv_nu_stop: - -cv:nu_stop $param_cv_nu_stop -#end if -#if $param_cv_sigma_start: - -cv:sigma_start $param_cv_sigma_start +#if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',') + && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset' #end if -#if $param_cv_sigma_step_size: - -cv:sigma_step_size $param_cv_sigma_step_size -#end if -#if $param_cv_sigma_stop: - -cv:sigma_stop $param_cv_sigma_stop -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +#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 name="param_in" type="data" format="idxml,txt" optional="True" label="This is the name of the input file (RT prediction)" help="(-in) 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. <br>"/> - <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/> - <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/> - <param name="param_svm_type" display="radio" type="select" optional="False" value="NU_SVR" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set <br>to C_SVC for separation prediction)" help="(-svm_type) "> + <param name="in" 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 name="in_positive" 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 name="in_negative" 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 name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" 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"/> </param> - <param name="param_nu" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help="(-nu) "/> - <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p) "/> - <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/> - <param name="param_kernel_type" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) "> + <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=""/> + <param name="p" argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/> + <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/> + <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" 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"/> </param> - <param name="param_degree" type="integer" min="1" optional="True" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help="(-degree) "/> - <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/> - <param name="param_max_std" type="float" min="0.0" optional="True" 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="(-max_std) "/> - <param name="param_k_mer_length" type="integer" min="1" optional="True" value="1" label="k_mer length of the POBK" help="(-k_mer_length) "/> - <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/> - <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help="(-total_gradient_time) "/> - <param name="param_first_dim_rt" display="radio" type="boolean" truevalue="-first_dim_rt" falsevalue="" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt) "/> - <param name="param_additive_cv" display="radio" type="boolean" truevalue="-additive_cv" falsevalue="" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied <br>with the step size to get the new value" help="(-additive_cv) "/> - <param name="param_cv_skip_cv" display="radio" type="boolean" truevalue="-cv:skip_cv" falsevalue="" checked="false" optional="True" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help="(-skip_cv) "/> - <param name="param_cv_number_of_runs" type="integer" min="1" optional="True" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help="(-number_of_runs) "/> - <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/> - <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/> - <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/> - <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/> - <param name="param_cv_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start) "/> - <param name="param_cv_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size) "/> - <param name="param_cv_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop) "/> - <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/> - <param name="param_cv_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size) "/> - <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/> - <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/> - <param name="param_cv_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size) "/> - <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop) "/> - <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/> - <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/> - <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/> - <expand macro="advanced_options"> - <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <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=""/> + <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/> + <param name="max_std" 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 name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/> + <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/> + <param name="total_gradient_time" 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 name="first_dim_rt" 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 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" 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 name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> + </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="out_oligo_params_FLAG">out_oligo_params (stopping point of sigma)</option> + <option value="out_oligo_trainset_FLAG">out_oligo_trainset (stopping point of sigma)</option> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="txt"/> - <data name="param_out_oligo_params" format="paramXML"/> - <data name="param_out_oligo_trainset" format="txt"/> + <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> - <help>Trains a model for the retention time prediction of peptides from a training set. + <tests> + <expand macro="autotest_RTModel"/> + <expand macro="manutest_RTModel"/> + </tests> + <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_RTModel.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_RTModel.html]]></help> + <expand macro="references"/> </tool>