Mercurial > repos > galaxyp > openms_epifany
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 |
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date | Fri, 14 Jun 2024 21:32:01 +0000 |
parents | f3096a586de8 |
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4:f3096a586de8 | 5:e8c52c1d6f98 |
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1 <?xml version='1.0' encoding='UTF-8'?> | |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | 1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Utilities]--> | 2 <!--Proposed Tool Section: [Identification Processing]--> |
4 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Runs a Bayesian protein inference.</description> | 4 <description>Runs a Bayesian protein inference</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">Epifany</token> | 6 <token name="@EXECUTABLE@">Epifany</token> |
8 <import>macros.xml</import> | 7 <import>macros.xml</import> |
9 </macros> | 8 </macros> |
10 <expand macro="requirements"/> | 9 <expand macro="requirements"/> |
15 | 14 |
16 ## Preprocessing | 15 ## Preprocessing |
17 mkdir in_cond.in && | 16 mkdir in_cond.in && |
18 #if $in_cond.in_select == "no" | 17 #if $in_cond.in_select == "no" |
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && | 18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && |
20 ${' '.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])} | 19 ${' '.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])} |
21 #else | 20 #else |
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && | 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && |
23 #end if | 22 #end if |
24 #if $exp_design: | 23 #if $exp_design: |
25 mkdir exp_design && | 24 mkdir exp_design && |
26 ln -s '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && | 25 cp '$exp_design' 'exp_design/${re.sub("[^\w\-_]", "_", $exp_design.element_identifier)}.$gxy2omsext($exp_design.ext)' && |
27 #end if | 26 #end if |
28 mkdir out && | 27 mkdir out && |
29 | 28 |
30 ## Main program call | 29 ## Main program call |
31 | 30 |
60 <param name="in_select" type="select" label="Run tool in batch mode for -in"> | 59 <param name="in_select" type="select" label="Run tool in batch mode for -in"> |
61 <option value="no">No: process all datasets jointly</option> | 60 <option value="no">No: process all datasets jointly</option> |
62 <option value="yes">Yes: process each dataset in an independent job</option> | 61 <option value="yes">Yes: process each dataset in an independent job</option> |
63 </param> | 62 </param> |
64 <when value="no"> | 63 <when value="no"> |
65 <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> | 64 <param argument="-in" type="data" format="consensusxml,idxml" multiple="true" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> |
66 </when> | 65 </when> |
67 <when value="yes"> | 66 <when value="yes"> |
68 <param argument="-in" type="data" format="consensusxml,idxml" multiple="false" optional="false" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> | 67 <param argument="-in" type="data" format="consensusxml,idxml" label="Input: identification results" help=" select consensusxml,idxml data sets(s)"/> |
69 </when> | 68 </when> |
70 </conditional> | 69 </conditional> |
71 <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/> | 70 <param argument="-exp_design" type="data" format="tabular" optional="true" label="(Currently unused) Input: experimental design" help=" select tabular data sets(s)"/> |
72 <param argument="-out_type" display="radio" type="select" optional="false" label="Output type: auto detected by file extension but can be overwritten here" help=""> | 71 <param argument="-out_type" type="select" label="Output type: auto detected by file extension but can be overwritten here" help=""> |
73 <option value="consensusXML">consensusxml</option> | 72 <option value="consensusXML">consensusxml</option> |
74 <option value="idXML">idxml</option> | 73 <option value="idXML">idxml</option> |
74 <validator type="expression" message="A value needs to be selected">value != "select a value"</validator> | |
75 <expand macro="list_string_san" name="out_type"/> | 75 <expand macro="list_string_san" name="out_type"/> |
76 </param> | 76 </param> |
77 <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=""/> | 77 <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=""/> |
78 <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"> | 78 <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"> |
79 <option value="none" selected="true">none</option> | 79 <option value="none" selected="true">none</option> |
80 <option value="remove_associations_only">remove_associations_only</option> | 80 <option value="remove_associations_only">remove_associations_only</option> |
81 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> | 81 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option> |
82 <expand macro="list_string_san" name="greedy_group_resolution"/> | 82 <expand macro="list_string_san" name="greedy_group_resolution"/> |
83 </param> | 83 </param> |
84 <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=""/> | 84 <param argument="-max_psms_extreme_probability" type="float" value="1.0" label="Set PSMs with probability higher than this to this maximum probability" help=""/> |
85 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false"> | 85 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false"> |
86 <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=""/> | 86 <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=""/> |
87 <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"/> | 87 <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"/> |
88 <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?"/> | 88 <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?"/> |
89 <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=""/> | 89 <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=""/> |
90 <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=""/> | 90 <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=""/> |
91 <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=""/> | 91 <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=""/> |
92 <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=""/> | 92 <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=""/> |
93 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false"> | 93 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false"> |
94 <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"/> | 94 <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"/> |
95 <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"/> | 95 <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"/> |
96 <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"/> | 96 <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"/> |
97 <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=""/> | 97 <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=""/> |
98 <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=""/> | 98 <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=""/> |
99 <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=""/> | 99 <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=""/> |
100 </section> | 100 </section> |
101 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false"> | 101 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false"> |
102 <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"> | 102 <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"> |
103 <option value="priority" selected="true">priority</option> | 103 <option value="priority" selected="true">priority</option> |
104 <option value="fifo">fifo</option> | 104 <option value="fifo">fifo</option> |
105 <option value="subtree">subtree</option> | 105 <option value="subtree">subtree</option> |
106 <expand macro="list_string_san" name="scheduling_type"/> | 106 <expand macro="list_string_san" name="scheduling_type"/> |
107 </param> | 107 </param> |
108 <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=""/> | 108 <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=""/> |
109 <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"/> | 109 <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"/> |
110 <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?"/> | 110 <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?"/> |
111 <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),<= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/> | 111 <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),<= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get"/> |
112 </section> | 112 </section> |
113 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false"> | 113 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false"> |
114 <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"/> | 114 <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"/> |
115 <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=""/> | 115 <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=""/> |
116 <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=""/> | 116 <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=""/> |
117 </section> | 117 </section> |
118 </section> | 118 </section> |
119 <expand macro="adv_opts_macro"> | 119 <expand macro="adv_opts_macro"> |
120 <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=""/> | 120 <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=""/> |
121 <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/> | 121 <param argument="-picked_fdr" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use picked protein FDRs" help=""/> |
122 <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"> | 122 <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"> |
123 <expand macro="list_string_san" name="picked_decoy_string"/> | 123 <expand macro="list_string_san" name="picked_decoy_string"/> |
124 </param> | 124 </param> |
125 <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"> | 125 <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"> |
126 <option value="prefix" selected="true">prefix</option> | 126 <option value="prefix" selected="true">prefix</option> |
127 <option value="suffix">suffix</option> | 127 <option value="suffix">suffix</option> |
128 <expand macro="list_string_san" name="picked_decoy_prefix"/> | 128 <expand macro="list_string_san" name="picked_decoy_prefix"/> |
129 </param> | 129 </param> |
130 <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=""/> | 130 <param argument="-min_psms_extreme_probability" type="float" value="0.0" label="Set PSMs with probability lower than this to this minimum probability" help=""/> |
131 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 131 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
132 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 132 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
133 <expand macro="list_string_san" name="test"/> | 133 <expand macro="list_string_san" name="test"/> |
134 </param> | 134 </param> |
135 </expand> | 135 </expand> |
136 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 136 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
137 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 137 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
145 </data> | 145 </data> |
146 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 146 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
147 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 147 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
148 </data> | 148 </data> |
149 </outputs> | 149 </outputs> |
150 <tests><!-- UTILS_Epifany_1 --> | 150 <tests> |
151 <!-- TOPP_Epifany_1 --> | |
151 <test expect_num_outputs="2"> | 152 <test expect_num_outputs="2"> |
152 <section name="adv_opts"> | 153 <section name="adv_opts"> |
153 <param name="conservative_fdr" value="true"/> | 154 <param name="conservative_fdr" value="true"/> |
154 <param name="picked_fdr" value="true"/> | 155 <param name="picked_fdr" value="true"/> |
155 <param name="picked_decoy_string" value=""/> | 156 <param name="picked_decoy_string" value=""/> |
159 <param name="test" value="true"/> | 160 <param name="test" value="true"/> |
160 </section> | 161 </section> |
161 <conditional name="in_cond"> | 162 <conditional name="in_cond"> |
162 <param name="in" value="FidoAdapter_1_input.idXML"/> | 163 <param name="in" value="FidoAdapter_1_input.idXML"/> |
163 </conditional> | 164 </conditional> |
164 <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> | 165 <output name="out" value="Epifany_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
165 <param name="out_type" value="idXML"/> | 166 <param name="out_type" value="idXML"/> |
166 <param name="protein_fdr" value="false"/> | 167 <param name="protein_fdr" value="false"/> |
167 <param name="greedy_group_resolution" value="none"/> | 168 <param name="greedy_group_resolution" value="none"/> |
168 <param name="max_psms_extreme_probability" value="1.0"/> | 169 <param name="max_psms_extreme_probability" value="1.0"/> |
169 <section name="algorithm"> | 170 <section name="algorithm"> |
199 <output name="ctd_out" ftype="xml"> | 200 <output name="ctd_out" ftype="xml"> |
200 <assert_contents> | 201 <assert_contents> |
201 <is_valid_xml/> | 202 <is_valid_xml/> |
202 </assert_contents> | 203 </assert_contents> |
203 </output> | 204 </output> |
205 <assert_stdout> | |
206 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
207 </assert_stdout> | |
204 </test> | 208 </test> |
205 <!-- UTILS_Epifany_2 --> | 209 <!-- TOPP_Epifany_2 --> |
206 <test expect_num_outputs="2"> | 210 <test expect_num_outputs="2"> |
207 <section name="adv_opts"> | 211 <section name="adv_opts"> |
208 <param name="conservative_fdr" value="true"/> | 212 <param name="conservative_fdr" value="true"/> |
209 <param name="picked_fdr" value="true"/> | 213 <param name="picked_fdr" value="true"/> |
210 <param name="picked_decoy_string" value=""/> | 214 <param name="picked_decoy_string" value=""/> |
214 <param name="test" value="true"/> | 218 <param name="test" value="true"/> |
215 </section> | 219 </section> |
216 <conditional name="in_cond"> | 220 <conditional name="in_cond"> |
217 <param name="in" value="Epifany_2_input.consensusXML"/> | 221 <param name="in" value="Epifany_2_input.consensusXML"/> |
218 </conditional> | 222 </conditional> |
219 <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | 223 <output name="out" value="Epifany_2_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
220 <param name="out_type" value="consensusXML"/> | 224 <param name="out_type" value="consensusXML"/> |
221 <param name="protein_fdr" value="false"/> | 225 <param name="protein_fdr" value="false"/> |
222 <param name="greedy_group_resolution" value="none"/> | 226 <param name="greedy_group_resolution" value="none"/> |
223 <param name="max_psms_extreme_probability" value="1.0"/> | 227 <param name="max_psms_extreme_probability" value="1.0"/> |
224 <section name="algorithm"> | 228 <section name="algorithm"> |
254 <output name="ctd_out" ftype="xml"> | 258 <output name="ctd_out" ftype="xml"> |
255 <assert_contents> | 259 <assert_contents> |
256 <is_valid_xml/> | 260 <is_valid_xml/> |
257 </assert_contents> | 261 </assert_contents> |
258 </output> | 262 </output> |
263 <assert_stdout> | |
264 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
265 </assert_stdout> | |
259 </test> | 266 </test> |
260 <!-- UTILS_Epifany_3 --> | 267 <!-- TOPP_Epifany_3 --> |
261 <test expect_num_outputs="2"> | 268 <test expect_num_outputs="2"> |
262 <section name="adv_opts"> | 269 <section name="adv_opts"> |
263 <param name="conservative_fdr" value="true"/> | 270 <param name="conservative_fdr" value="true"/> |
264 <param name="picked_fdr" value="true"/> | 271 <param name="picked_fdr" value="true"/> |
265 <param name="picked_decoy_string" value=""/> | 272 <param name="picked_decoy_string" value=""/> |
269 <param name="test" value="true"/> | 276 <param name="test" value="true"/> |
270 </section> | 277 </section> |
271 <conditional name="in_cond"> | 278 <conditional name="in_cond"> |
272 <param name="in" value="Epifany_2_input.consensusXML"/> | 279 <param name="in" value="Epifany_2_input.consensusXML"/> |
273 </conditional> | 280 </conditional> |
274 <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> | 281 <output name="out" value="Epifany_3_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/> |
275 <param name="out_type" value="consensusXML"/> | 282 <param name="out_type" value="consensusXML"/> |
276 <param name="protein_fdr" value="false"/> | 283 <param name="protein_fdr" value="false"/> |
277 <param name="greedy_group_resolution" value="none"/> | 284 <param name="greedy_group_resolution" value="none"/> |
278 <param name="max_psms_extreme_probability" value="1.0"/> | 285 <param name="max_psms_extreme_probability" value="1.0"/> |
279 <section name="algorithm"> | 286 <section name="algorithm"> |
309 <output name="ctd_out" ftype="xml"> | 316 <output name="ctd_out" ftype="xml"> |
310 <assert_contents> | 317 <assert_contents> |
311 <is_valid_xml/> | 318 <is_valid_xml/> |
312 </assert_contents> | 319 </assert_contents> |
313 </output> | 320 </output> |
321 <assert_stdout> | |
322 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
323 </assert_stdout> | |
314 </test> | 324 </test> |
315 <!-- UTILS_Epifany_4 --> | 325 <!-- TOPP_Epifany_4 --> |
316 <test expect_num_outputs="2"> | 326 <test expect_num_outputs="2"> |
317 <section name="adv_opts"> | 327 <section name="adv_opts"> |
318 <param name="conservative_fdr" value="true"/> | 328 <param name="conservative_fdr" value="true"/> |
319 <param name="picked_fdr" value="true"/> | 329 <param name="picked_fdr" value="true"/> |
320 <param name="picked_decoy_string" value=""/> | 330 <param name="picked_decoy_string" value=""/> |
324 <param name="test" value="true"/> | 334 <param name="test" value="true"/> |
325 </section> | 335 </section> |
326 <conditional name="in_cond"> | 336 <conditional name="in_cond"> |
327 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> | 337 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> |
328 </conditional> | 338 </conditional> |
329 <output name="out" file="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> | 339 <output name="out" value="Epifany_4_out_singlerun.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
330 <param name="out_type" value="idXML"/> | 340 <param name="out_type" value="idXML"/> |
331 <param name="protein_fdr" value="false"/> | 341 <param name="protein_fdr" value="false"/> |
332 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> | 342 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> |
333 <param name="max_psms_extreme_probability" value="1.0"/> | 343 <param name="max_psms_extreme_probability" value="1.0"/> |
334 <section name="algorithm"> | 344 <section name="algorithm"> |
364 <output name="ctd_out" ftype="xml"> | 374 <output name="ctd_out" ftype="xml"> |
365 <assert_contents> | 375 <assert_contents> |
366 <is_valid_xml/> | 376 <is_valid_xml/> |
367 </assert_contents> | 377 </assert_contents> |
368 </output> | 378 </output> |
379 <assert_stdout> | |
380 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
381 </assert_stdout> | |
369 </test> | 382 </test> |
370 <!-- UTILS_Epifany_5 --> | 383 <!-- TOPP_Epifany_5 --> |
371 <test expect_num_outputs="2"> | 384 <test expect_num_outputs="2"> |
372 <section name="adv_opts"> | 385 <section name="adv_opts"> |
373 <param name="conservative_fdr" value="true"/> | 386 <param name="conservative_fdr" value="true"/> |
374 <param name="picked_fdr" value="false"/> | 387 <param name="picked_fdr" value="false"/> |
375 <param name="picked_decoy_string" value=""/> | 388 <param name="picked_decoy_string" value=""/> |
379 <param name="test" value="true"/> | 392 <param name="test" value="true"/> |
380 </section> | 393 </section> |
381 <conditional name="in_cond"> | 394 <conditional name="in_cond"> |
382 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> | 395 <param name="in" value="FidoAdapter_1_input_singlerun.idXML"/> |
383 </conditional> | 396 </conditional> |
384 <output name="out" file="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> | 397 <output name="out" value="Epifany_4_out_singlerun_fdr.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> |
385 <param name="out_type" value="idXML"/> | 398 <param name="out_type" value="idXML"/> |
386 <param name="protein_fdr" value="true"/> | 399 <param name="protein_fdr" value="true"/> |
387 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> | 400 <param name="greedy_group_resolution" value="remove_proteins_wo_evidence"/> |
388 <param name="max_psms_extreme_probability" value="1.0"/> | 401 <param name="max_psms_extreme_probability" value="1.0"/> |
389 <section name="algorithm"> | 402 <section name="algorithm"> |
419 <output name="ctd_out" ftype="xml"> | 432 <output name="ctd_out" ftype="xml"> |
420 <assert_contents> | 433 <assert_contents> |
421 <is_valid_xml/> | 434 <is_valid_xml/> |
422 </assert_contents> | 435 </assert_contents> |
423 </output> | 436 </output> |
437 <assert_stdout> | |
438 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> | |
439 </assert_stdout> | |
424 </test> | 440 </test> |
425 </tests> | 441 </tests> |
426 <help><![CDATA[Runs a Bayesian protein inference. | 442 <help><![CDATA[Runs a Bayesian protein inference. |
427 | 443 |
428 | 444 |
429 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_Epifany.html]]></help> | 445 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_Epifany.html]]></help> |
430 <expand macro="references"/> | 446 <expand macro="references"/> |
431 </tool> | 447 </tool> |