Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

annotate IDPosteriorErrorProbability.xml @ 10:18ee86db4af2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:10:31 +0000
parents 5d9f175dff81
children 711a081d80ba
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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: [ID Processing]-->
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4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</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 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_plot &&
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24 #end if
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26 ## Main program call
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28 set -o pipefail &&
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29 @EXECUTABLE@ -write_ctd ./ &&
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30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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32 -in
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33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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34 -out
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35 'out/output.${gxy2omsext("idxml")}'
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36 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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37 -out_plot
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38 'out_plot/output.${gxy2omsext("txt")}'
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39 #end if
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40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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41 | tee '$stdout'
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42 #end if
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44 ## Postprocessing
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45 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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46 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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47 && mv 'out_plot/output.${gxy2omsext("txt")}' '$out_plot'
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48 #end if
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49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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50 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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51 #end if]]></command>
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52 <configfiles>
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53 <inputs name="args_json" data_style="paths"/>
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54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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55 </configfiles>
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56 <inputs>
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57 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
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58 <param name="split_charge" argument="-split_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="The search engine scores are split by charge if this flag is set" help="Thus, for each charge state a new model will be computed"/>
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59 <param name="top_hits_only" argument="-top_hits_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set only the top hits of every PeptideIdentification will be used" help=""/>
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60 <param name="ignore_bad_data" argument="-ignore_bad_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set errors will be written but ignored" help="Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/>
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61 <param name="prob_correct" argument="-prob_correct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help=""/>
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62 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false">
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63 <param name="number_of_bins" argument="-fit_algorithm:number_of_bins" type="integer" optional="true" value="100" label="Number of bins used for visualization" help="Only needed if each iteration step of the EM-Algorithm will be visualized"/>
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64 <param name="incorrectly_assigned" argument="-fit_algorithm:incorrectly_assigned" display="radio" type="select" optional="false" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="For 'Gauss', the Gauss distribution is used">
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65 <option value="Gumbel" selected="true">Gumbel</option>
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66 <option value="Gauss">Gauss</option>
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67 <expand macro="list_string_san"/>
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68 </param>
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69 <param name="max_nr_iterations" argument="-fit_algorithm:max_nr_iterations" type="integer" optional="true" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help=""/>
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70 <param name="neg_log_delta" argument="-fit_algorithm:neg_log_delta" type="integer" optional="true" value="6" label="The negative logarithm of the convergence threshold for the likelihood increase" help=""/>
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71 <param name="outlier_handling" argument="-fit_algorithm:outlier_handling" display="radio" type="select" optional="false" label="What to do with outliers:" help="- ignore_iqr_outliers: ignore outliers outside of 3*IQR from Q1/Q3 for fitting. - set_iqr_to_closest_valid: set IQR-based outliers to the last valid value for fitting. - ignore_extreme_percentiles: ignore everything outside 99th and 1st percentile (also removes equal values like potential censored max values in XTandem). - none: do nothing">
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72 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option>
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73 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option>
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74 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option>
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75 <option value="none">none</option>
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76 <expand macro="list_string_san"/>
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77 </param>
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78 </section>
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79 <expand macro="adv_opts_macro">
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80 <param name="fdr_for_targets_smaller" argument="-fdr_for_targets_smaller" type="float" optional="true" value="0.05" label="Only used, when top_hits_only set" help="Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/>
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81 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
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82 <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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83 <expand macro="list_string_san"/>
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84 </param>
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85 </expand>
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86 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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87 <option value="out_plot_FLAG">out_plot (What to do with outliers:)</option>
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88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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93 <data name="out_plot" label="${tool.name} on ${on_string}: out_plot" format="txt">
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94 <filter>OPTIONAL_OUTPUTS is not None and "out_plot_FLAG" in OPTIONAL_OUTPUTS</filter>
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95 </data>
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96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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98 </data>
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99 </outputs>
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100 <tests>
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101 <expand macro="autotest_IDPosteriorErrorProbability"/>
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102 <expand macro="manutest_IDPosteriorErrorProbability"/>
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103 </tests>
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104 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
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105
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106
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107 For more information, visit http://www.openms.de/documentation/TOPP_IDPosteriorErrorProbability.html]]></help>
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108 <expand macro="references"/>
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109 </tool>