openms_epifany: Epifany.xml comparison

comparison Epifany.xml @ 5:e8c52c1d6f98 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

author	galaxyp
date	Fri, 14 Jun 2024 21:32:01 +0000
parents	f3096a586de8
children

comparison

equal deleted inserted replaced

-:f3096a586de8
+:e8c52c1d6f98
-<?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: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-<description>Runs a Bayesian protein inference.</description>
+<description>Runs a Bayesian protein inference</description>
 <macros>
 <token name="@EXECUTABLE@">Epifany</token>
 <import>macros.xml</import>
 </macros>
 <expand macro="requirements"/>
 ## Preprocessing
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 #if $exp_design:
 mkdir exp_design &&
-ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
+cp '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' &&
 #end if
 mkdir out &&
 ## Main program call
 <param name="in_select" type="select" label="Run tool in batch mode for -in">
 <option value="no">No: process all datasets jointly</option>
 <option value="yes">Yes: process each dataset in an independent job</option>
 </param>
 <when value="no">
-<param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+<param argument="-in" type="data" format="consensusxml,idxml" multiple="true" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
 </when>
 <when value="yes">
-<param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
+<param argument="-in" type="data" format="consensusxml,idxml" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/>
 </when>
 </conditional>
 <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/>
-<param argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help="">
+<param argument="-out_type" type="select" label="Output type: auto detected by file extension but can be overwritten here" help="">
 <option value="consensusXML">consensusxml</option>
 <option value="idXML">idxml</option>
+<validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
 <expand macro="list_string_san" name="out_type"/>
 </param>
 <param argument="-protein_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Additionally calculate the target-decoy FDR on protein-level based on the posteriors" help=""/>
-<param argument="-greedy_group_resolution" type="select" optional="true" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
+<param argument="-greedy_group_resolution" type="select" label="Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities" help="Also adds the resolved ambiguity groups to output">
 <option value="none" selected="true">none</option>
 <option value="remove_associations_only">remove_associations_only</option>
 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option>
 <expand macro="list_string_san" name="greedy_group_resolution"/>
 </param>
-<param argument="-max_psms_extreme_probability" type="float" optional="true" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
+<param argument="-max_psms_extreme_probability" type="float" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/>
 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false">
-<param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" optional="true" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/>
+<param name="psm_probability_cutoff" argument="-algorithm:psm_probability_cutoff" type="float" min="0.0" max="1.0" value="0.001" label="Remove PSMs with probabilities less than this cutoff" help=""/>
-<param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" optional="true" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/>
+<param name="top_PSMs" argument="-algorithm:top_PSMs" type="integer" min="0" value="1" label="Consider only top X PSMs per spectrum" help="0 considers all"/>
 <param name="keep_best_PSM_only" argument="-algorithm:keep_best_PSM_only" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Epifany uses the best PSM per peptide for inference" help="Discard the rest (true) or keepe.g. for quantification/reporting?"/>
 <param name="update_PSM_probabilities" argument="-algorithm:update_PSM_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities" help=""/>
 <param name="user_defined_priors" argument="-algorithm:user_defined_priors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Experimental:) Uses the current protein scores as user-defined priors" help=""/>
 <param name="annotate_group_probabilities" argument="-algorithm:annotate_group_probabilities" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Annotates group probabilities for indistinguishable protein groups (indistinguishable by experimentally observed PSMs)" help=""/>
 <param name="use_ids_outside_features" argument="-algorithm:use_ids_outside_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="(Only consensusXML) Also use IDs without associated features for inference?" help=""/>
 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false">
-<param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/>
+<param name="prot_prior" argument="-algorithm:model_parameters:prot_prior" type="float" min="-1.0" max="1.0" value="-1.0" label="Protein prior probability ('gamma' parameter)" help="Negative values enable grid search for this param"/>
-<param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/>
+<param name="pep_emission" argument="-algorithm:model_parameters:pep_emission" type="float" min="-1.0" max="1.0" value="-1.0" label="Peptide emission probability ('alpha' parameter)" help="Negative values enable grid search for this param"/>
-<param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/>
+<param name="pep_spurious_emission" argument="-algorithm:model_parameters:pep_spurious_emission" type="float" min="-1.0" max="1.0" value="-1.0" label="Spurious peptide identification probability ('beta' parameter)" help="Usually much smaller than emission from proteins. Negative values enable grid search for this param"/>
-<param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/>
+<param name="pep_prior" argument="-algorithm:model_parameters:pep_prior" type="float" min="0.0" max="1.0" value="0.1" label="Peptide prior probability (experimental, should be covered by combinations of the other params)" help=""/>
 <param name="regularize" argument="-algorithm:model_parameters:regularize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Regularize the number of proteins that produce a peptide together (experimental, should be activated when using higher p-norms)" help=""/>
 <param name="extended_model" argument="-algorithm:model_parameters:extended_model" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)" help=""/>
 </section>
 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false">
-<param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" optional="true" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
+<param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" type="select" label="(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important)" help="fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration">
 <option value="priority" selected="true">priority</option>
 <option value="fifo">fifo</option>
 <option value="subtree">subtree</option>
 <expand macro="list_string_san" name="scheduling_type"/>
 </param>
-<param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
+<param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" min="0.0" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
-<param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" optional="true" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/>
+<param name="dampening_lambda" argument="-algorithm:loopy_belief_propagation:dampening_lambda" type="float" min="0.0" max="0.49999" value="0.001" label="Initial value for how strongly should messages be updated in each step" help="0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence"/>
-<param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/>
+<param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" value="2147483647" label="(Usually auto-determined by estimated but you can set a hard limit here)" help="If not all messages converge, how many iterations should be done at max per connected component?"/>
-<param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" optional="true" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),&lt;= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/>
+<param name="p_norm_inference" argument="-algorithm:loopy_belief_propagation:p_norm_inference" type="float" value="1.0" label="P-norm used for marginalization of multidimensional factors" help="1 == sum-product inference (all configurations vote equally) (default),&lt;= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/>
 </section>
 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false">
-<param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="How important is target decoy AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/>
+<param name="aucweight" argument="-algorithm:param_optimize:aucweight" type="float" min="0.0" max="1.0" value="0.3" label="How important is target decoy AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/>
 <param name="conservative_fdr" argument="-algorithm:param_optimize:conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for parameter estimation" help=""/>
 <param name="regularized_fdr" argument="-algorithm:param_optimize:regularized_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use a regularized FDR for proteins without unique peptides" help=""/>
 </section>
 </section>
 <expand macro="adv_opts_macro">
 <param argument="-conservative_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs" help=""/>
 <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/>
 <param argument="-picked_decoy_string" type="text" optional="true" value="" label="If using picked protein FDRs, which decoy string was used" help="Leave blank for auto-detection">
 <expand macro="list_string_san" name="picked_decoy_string"/>
 </param>
-<param argument="-picked_decoy_prefix" type="select" optional="true" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
+<param argument="-picked_decoy_prefix" type="select" label="If using picked protein FDRs, was the decoy string a prefix or suffix" help="Ignored during auto-detection">
 <option value="prefix" selected="true">prefix</option>
 <option value="suffix">suffix</option>
 <expand macro="list_string_san" name="picked_decoy_prefix"/>
 </param>
-<param argument="-min_psms_extreme_probability" type="float" optional="true" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
+<param argument="-min_psms_extreme_probability" type="float" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/>
 <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="">
+<param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
 <expand macro="list_string_san" name="test"/>
 </param>
 </expand>
 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
 </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><!-- UTILS_Epifany_1 -->
+<tests>
+<!-- TOPP_Epifany_1 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="conservative_fdr" value="true"/>
 <param name="picked_fdr" value="true"/>
 <param name="picked_decoy_string" value=""/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="FidoAdapter_1_input.idXML"/>
 </conditional>
-<output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="out_type" value="idXML"/>
 <param name="protein_fdr" value="false"/>
 <param name="greedy_group_resolution" value="none"/>
 <param name="max_psms_extreme_probability" value="1.0"/>
 <section name="algorithm">
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
-<!-- UTILS_Epifany_2 -->
+<!-- TOPP_Epifany_2 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="conservative_fdr" value="true"/>
 <param name="picked_fdr" value="true"/>
 <param name="picked_decoy_string" value=""/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="Epifany_2_input.consensusXML"/>
 </conditional>
-<output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+<output name="out" value="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
 <param name="out_type" value="consensusXML"/>
 <param name="protein_fdr" value="false"/>
 <param name="greedy_group_resolution" value="none"/>
 <param name="max_psms_extreme_probability" value="1.0"/>
 <section name="algorithm">
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
-<!-- UTILS_Epifany_3 -->
+<!-- TOPP_Epifany_3 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="conservative_fdr" value="true"/>
 <param name="picked_fdr" value="true"/>
 <param name="picked_decoy_string" value=""/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="Epifany_2_input.consensusXML"/>
 </conditional>
-<output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+<output name="out" value="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
 <param name="out_type" value="consensusXML"/>
 <param name="protein_fdr" value="false"/>
 <param name="greedy_group_resolution" value="none"/>
 <param name="max_psms_extreme_probability" value="1.0"/>
 <section name="algorithm">
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
-<!-- UTILS_Epifany_4 -->
+<!-- TOPP_Epifany_4 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="conservative_fdr" value="true"/>
 <param name="picked_fdr" value="true"/>
 <param name="picked_decoy_string" value=""/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
 </conditional>
-<output name="out" file="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="out_type" value="idXML"/>
 <param name="protein_fdr" value="false"/>
 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
 <param name="max_psms_extreme_probability" value="1.0"/>
 <section name="algorithm">
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
-<!-- UTILS_Epifany_5 -->
+<!-- TOPP_Epifany_5 -->
 <test expect_num_outputs="2">
 <section name="adv_opts">
 <param name="conservative_fdr" value="true"/>
 <param name="picked_fdr" value="false"/>
 <param name="picked_decoy_string" value=""/>
 <param name="test" value="true"/>
 </section>
 <conditional name="in_cond">
 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/>
 </conditional>
-<output name="out" file="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+<output name="out" value="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
 <param name="out_type" value="idXML"/>
 <param name="protein_fdr" value="true"/>
 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/>
 <param name="max_psms_extreme_probability" value="1.0"/>
 <section name="algorithm">
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <is_valid_xml/>
 </assert_contents>
 </output>
+<assert_stdout>
+<has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+</assert_stdout>
 </test>
 </tests>
 <help><![CDATA[Runs a Bayesian protein inference.
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Epifany.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Epifany.html]]></help>
 <expand macro="references"/>
 </tool>

Mercurial > repos > galaxyp > openms_epifany

comparison Epifany.xml @ 5:e8c52c1d6f98 draft default tip