Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
comparison IDPosteriorErrorProbability.xml @ 10:18ee86db4af2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 20:10:31 +0000 |
parents | 5d9f175dff81 |
children | 711a081d80ba |
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9:5d9f175dff81 | 10:18ee86db4af2 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 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.--> | 2 <!--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: [ID Processing]--> | 3 <!--Proposed Tool Section: [ID Processing]--> |
4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.3.0"> | 4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description> | 5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> | 7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
9 </macros> | 11 </macros> |
10 <expand macro="references"/> | 12 <expand macro="requirements"/> |
11 <expand macro="stdio"/> | 13 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
13 <command detect_errors="aggressive"><![CDATA[IDPosteriorErrorProbability | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 mkdir in && |
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
21 mkdir out && | |
22 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
23 mkdir out_plot && | |
17 #end if | 24 #end if |
18 #if $param_out: | 25 |
19 -out $param_out | 26 ## Main program call |
27 | |
28 set -o pipefail && | |
29 @EXECUTABLE@ -write_ctd ./ && | |
30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
32 -in | |
33 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
34 -out | |
35 'out/output.${gxy2omsext("idxml")}' | |
36 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
37 -out_plot | |
38 'out_plot/output.${gxy2omsext("txt")}' | |
20 #end if | 39 #end if |
21 #if $param_out_plot: | 40 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 |
22 -out_plot $param_out_plot | 41 | tee '$stdout' |
23 #end if | 42 #end if |
24 #if $param_split_charge: | 43 |
25 -split_charge | 44 ## Postprocessing |
45 && mv 'out/output.${gxy2omsext("idxml")}' '$out' | |
46 #if "out_plot_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
47 && mv 'out_plot/output.${gxy2omsext("txt")}' '$out_plot' | |
26 #end if | 48 #end if |
27 #if $param_top_hits_only: | 49 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
28 -top_hits_only | 50 && mv '@EXECUTABLE@.ctd' '$ctd_out' |
29 #end if | 51 #end if]]></command> |
30 #if $param_ignore_bad_data: | 52 <configfiles> |
31 -ignore_bad_data | 53 <inputs name="args_json" data_style="paths"/> |
32 #end if | 54 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
33 #if $param_prob_correct: | 55 </configfiles> |
34 -prob_correct | |
35 #end if | |
36 #if $adv_opts.adv_opts_selector=='advanced': | |
37 #if $adv_opts.param_fdr_for_targets_smaller: | |
38 -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller | |
39 #end if | |
40 #if $adv_opts.param_force: | |
41 -force | |
42 #end if | |
43 #if $adv_opts.param_fit_algorithm_number_of_bins: | |
44 -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins | |
45 #end if | |
46 #if $adv_opts.param_fit_algorithm_incorrectly_assigned: | |
47 -fit_algorithm:incorrectly_assigned | |
48 #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned): | |
49 "$adv_opts.param_fit_algorithm_incorrectly_assigned" | |
50 #else | |
51 $adv_opts.param_fit_algorithm_incorrectly_assigned | |
52 #end if | |
53 #end if | |
54 #if $adv_opts.param_fit_algorithm_max_nr_iterations: | |
55 -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations | |
56 #end if | |
57 #end if | |
58 ]]></command> | |
59 <inputs> | 56 <inputs> |
60 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> | 57 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> |
61 <param name="param_split_charge" display="radio" type="boolean" truevalue="-split_charge" falsevalue="" checked="false" optional="True" label="The search engine scores are split by charge if this flag is set" help="(-split_charge) Thus, for each charge state a new model will be computed"/> | 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"/> |
62 <param name="param_top_hits_only" display="radio" type="boolean" truevalue="-top_hits_only" falsevalue="" checked="false" optional="True" label="If set only the top hits of every PeptideIdentification will be used" help="(-top_hits_only) "/> | 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=""/> |
63 <param name="param_ignore_bad_data" display="radio" type="boolean" truevalue="-ignore_bad_data" falsevalue="" checked="false" optional="True" label="If set errors will be written but ignored" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through"/> | 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"/> |
64 <param name="param_prob_correct" display="radio" type="boolean" truevalue="-prob_correct" falsevalue="" checked="false" optional="True" label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" help="(-prob_correct) "/> | 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=""/> |
65 <expand macro="advanced_options"> | 62 <section name="fit_algorithm" title="Algorithm parameter subsection" help="" expanded="false"> |
66 <param name="param_fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set" help="(-fdr_for_targets_smaller) Additionally, target/decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run"/> | 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"/> |
67 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 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"> |
68 <param name="param_fit_algorithm_number_of_bins" type="integer" value="100" label="Number of bins used for visualization" help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized"/> | |
69 <param name="param_fit_algorithm_incorrectly_assigned" display="radio" type="select" optional="False" value="Gumbel" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used"> | |
70 <option value="Gumbel" selected="true">Gumbel</option> | 65 <option value="Gumbel" selected="true">Gumbel</option> |
71 <option value="Gauss">Gauss</option> | 66 <option value="Gauss">Gauss</option> |
67 <expand macro="list_string_san"/> | |
72 </param> | 68 </param> |
73 <param name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000" label="Bounds the number of iterations for the EM algorithm when convergence is slow" help="(-max_nr_iterations) "/> | 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=""/> |
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=""/> | |
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"> | |
72 <option value="ignore_iqr_outliers" selected="true">ignore_iqr_outliers</option> | |
73 <option value="set_iqr_to_closest_valid">set_iqr_to_closest_valid</option> | |
74 <option value="ignore_extreme_percentiles">ignore_extreme_percentiles</option> | |
75 <option value="none">none</option> | |
76 <expand macro="list_string_san"/> | |
77 </param> | |
78 </section> | |
79 <expand macro="adv_opts_macro"> | |
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"/> | |
81 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> | |
82 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
83 <expand macro="list_string_san"/> | |
84 </param> | |
74 </expand> | 85 </expand> |
86 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
87 <option value="out_plot_FLAG">out_plot (What to do with outliers:)</option> | |
88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
89 </param> | |
75 </inputs> | 90 </inputs> |
76 <outputs> | 91 <outputs> |
77 <data name="param_out" format="idxml"/> | 92 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
78 <data name="param_out_plot" format="txt"/> | 93 <data name="out_plot" label="${tool.name} on ${on_string}: out_plot" format="txt"> |
94 <filter>OPTIONAL_OUTPUTS is not None and "out_plot_FLAG" in OPTIONAL_OUTPUTS</filter> | |
95 </data> | |
96 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
97 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
98 </data> | |
79 </outputs> | 99 </outputs> |
80 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. | 100 <tests> |
101 <expand macro="autotest_IDPosteriorErrorProbability"/> | |
102 <expand macro="manutest_IDPosteriorErrorProbability"/> | |
103 </tests> | |
104 <help><![CDATA[Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. | |
81 | 105 |
82 | 106 |
83 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDPosteriorErrorProbability.html</help> | 107 For more information, visit http://www.openms.de/documentation/TOPP_IDPosteriorErrorProbability.html]]></help> |
108 <expand macro="references"/> | |
84 </tool> | 109 </tool> |