diff Epifany.xml @ 5:e8c52c1d6f98 draft default tip

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

--- a/Epifany.xml	Thu Dec 01 19:13:55 2022 +0000
+++ b/Epifany.xml	Fri Jun 14 21:32:01 2024 +0000
@@ -1,8 +1,7 @@
-<?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>
@@ -17,13 +16,13 @@
 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 &&
 
@@ -62,56 +61,57 @@
         <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="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="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" 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="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_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_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="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" 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" 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" 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="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="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="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="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" 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" 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" 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>
@@ -122,14 +122,14 @@
       <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>
@@ -147,7 +147,8 @@
       <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"/>
@@ -161,7 +162,7 @@
       <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"/>
@@ -201,8 +202,11 @@
           <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"/>
@@ -216,7 +220,7 @@
       <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"/>
@@ -256,8 +260,11 @@
           <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"/>
@@ -271,7 +278,7 @@
       <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"/>
@@ -311,8 +318,11 @@
           <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"/>
@@ -326,7 +336,7 @@
       <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"/>
@@ -366,8 +376,11 @@
           <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"/>
@@ -381,7 +394,7 @@
       <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"/>
@@ -421,11 +434,14 @@
           <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>