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annotate Epifany.xml @ 1:015b55cd3570 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:06:29 +0000
parents 03e13b23a78b
children 16cdef222ea2
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03e13b23a78b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="Epifany" name="Epifany" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Runs a Bayesian protein inference.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">Epifany</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir out &&
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22
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23 ## Main program call
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24
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25 set -o pipefail &&
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26 @EXECUTABLE@ -write_ctd ./ &&
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27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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29 -in
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30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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31 -out
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32 'out/output.${gxy2omsext("idxml")}'
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33
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34 ## Postprocessing
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35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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38 #end if]]></command>
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39 <configfiles>
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40 <inputs name="args_json" data_style="paths"/>
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41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/>
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45 <param name="protein_fdr" 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=""/>
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46 <param name="greedy_group_resolution" argument="-greedy_group_resolution" display="radio" type="select" optional="false" 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">
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47 <option value="none" selected="true">none</option>
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48 <option value="remove_associations_only">remove_associations_only</option>
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49 <option value="remove_proteins_wo_evidence">remove_proteins_wo_evidence</option>
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50 <expand macro="list_string_san"/>
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51 </param>
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52 <param name="max_psms_extreme_probability" 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=""/>
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53 <section name="algorithm" title="Parameters for the Algorithm section" help="" expanded="false">
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54 <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 or equal this cutoff" help=""/>
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55 <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"/>
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56 <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=""/>
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57 <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=""/>
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58 <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=""/>
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59 <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=""/>
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60 <section name="model_parameters" title="Model parameters for the Bayesian network" help="" expanded="false">
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61 <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"/>
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62 <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"/>
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63 <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"/>
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64 <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=""/>
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65 <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=""/>
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66 <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=""/>
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67 </section>
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68 <section name="loopy_belief_propagation" title="Settings for the loopy belief propagation algorithm" help="" expanded="false">
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69 <param name="scheduling_type" argument="-algorithm:loopy_belief_propagation:scheduling_type" display="radio" type="select" optional="false" 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. random_spanning_tree = message passing follows a random spanning tree in each iteration">
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70 <option value="priority" selected="true">priority</option>
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71 <option value="fifo">fifo</option>
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72 <option value="random_spanning_tree">random_spanning_tree</option>
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73 <expand macro="list_string_san"/>
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74 </param>
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75 <param name="convergence_threshold" argument="-algorithm:loopy_belief_propagation:convergence_threshold" type="float" optional="true" min="1e-09" max="1.0" value="1e-05" label="Initial threshold under which MSE difference a message is considered to be converged" help=""/>
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76 <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"/>
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77 <param name="max_nr_iterations" argument="-algorithm:loopy_belief_propagation:max_nr_iterations" type="integer" optional="true" value="2147483647" label="(Unused, autodetermined) If not all messages converge, how many iterations should be done at max?" help=""/>
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78 <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"/>
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79 </section>
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80 <section name="param_optimize" title="Settings for the parameter optimization" help="" expanded="false">
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81 <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 AUC vs calibration of the posteriors" help="0 = maximize calibration only, 1 = maximize AUC only, between = convex combination"/>
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82 <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=""/>
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83 </section>
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84 </section>
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85 <expand macro="adv_opts_macro">
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86 <param name="conservative_fdr" 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=""/>
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87 <param name="min_psms_extreme_probability" 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=""/>
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88 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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89 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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90 <expand macro="list_string_san"/>
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91 </param>
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92 </expand>
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93 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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94 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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95 </param>
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96 </inputs>
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97 <outputs>
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98 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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99 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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100 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <expand macro="autotest_Epifany"/>
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105 <expand macro="manutest_Epifany"/>
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106 </tests>
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107 <help><![CDATA[Runs a Bayesian protein inference.
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108
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109
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110 For more information, visit http://www.openms.de/documentation/UTILS_Epifany.html]]></help>
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111 <expand macro="references"/>
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112 </tool>