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comparison IDPosteriorErrorProbability.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <macros> 4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.0.0">
5 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token> 5 <description>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">IDPosteriorErrorProbability</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>IDPosteriorErrorProbability 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDPosteriorErrorProbability
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -out_plot ${param_out_plot} 17 #end if
15 ${param_split_charge} 18 #if $param_out:
16 ${param_top_hits_only} 19 -out $param_out
17 ${param_ignore_bad_data} 20 #end if
18 ${param_prob_correct} 21 #if $param_out_plot:
19 -threads \${GALAXY_SLOTS:-24} 22 -out_plot $param_out_plot
23 #end if
24 #if $param_split_charge:
25 -split_charge
26 #end if
27 #if $param_top_hits_only:
28 -top_hits_only
29 #end if
30 #if $param_ignore_bad_data:
31 -ignore_bad_data
32 #end if
33 #if $param_prob_correct:
34 -prob_correct
35 #end if
36 -threads \${GALAXY_SLOTS:-24}
20 #if $adv_opts.adv_opts_selector=='advanced': 37 #if $adv_opts.adv_opts_selector=='advanced':
21 -smallest_e_value ${adv_opts.param_smallest_e_value} 38 #if $adv_opts.param_fdr_for_targets_smaller:
22 -fdr_for_targets_smaller ${adv_opts.param_fdr_for_targets_smaller} 39 -fdr_for_targets_smaller $adv_opts.param_fdr_for_targets_smaller
23 -fit_algorithm:number_of_bins ${adv_opts.param_number_of_bins} 40 #end if
24 -fit_algorithm:incorrectly_assigned ${adv_opts.param_incorrectly_assigned} 41 #if $adv_opts.param_force:
42 -force
43 #end if
44 #if $adv_opts.param_fit_algorithm_number_of_bins:
45 -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
46 #end if
47 #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
48 -fit_algorithm:incorrectly_assigned
49 #if &quot; &quot; in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
50 &quot;$adv_opts.param_fit_algorithm_incorrectly_assigned&quot;
51 #else
52 $adv_opts.param_fit_algorithm_incorrectly_assigned
53 #end if
54 #end if
55 #if $adv_opts.param_fit_algorithm_max_nr_iterations:
56 -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
57 #end if
25 #end if 58 #end if
26 </command> 59 </command>
27 <inputs> 60 <inputs>
28 <param name="param_in" type="data" format="idXML" optional="False" label="input file " help="(-in)"/> 61 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
29 <param name="param_split_charge" type="boolean" truevalue="-split_charge true" falsevalue="-split_charge false" checked="false" optional="True" label="The search engine scores are split by charge if this flag is set. Thus, for each charge state a new model will be computed." help="(-split_charge)"/> 62 <param checked="false" falsevalue="" help="(-split_charge) Thus, for each charge state a new model will be computed" label="The search engine scores are split by charge if this flag is set" name="param_split_charge" optional="True" truevalue="-split_charge" type="boolean"/>
30 <param name="param_top_hits_only" type="boolean" truevalue="-top_hits_only true" falsevalue="-top_hits_only false" checked="false" optional="True" label="If set only the top hits of every PeptideIdentification will be used" help="(-top_hits_only)"/> 63 <param checked="false" falsevalue="" help="(-top_hits_only) " label="If set only the top hits of every PeptideIdentification will be used" name="param_top_hits_only" optional="True" truevalue="-top_hits_only" type="boolean"/>
31 <param name="param_ignore_bad_data" type="boolean" truevalue="-ignore_bad_data true" falsevalue="-ignore_bad_data false" checked="false" optional="True" label="If set errors will be written but ignored. Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through." help="(-ignore_bad_data)"/> 64 <param checked="false" falsevalue="" help="(-ignore_bad_data) Useful for pipelines with many datasets where only a few are bad, but the pipeline should run through" label="If set errors will be written but ignored" name="param_ignore_bad_data" optional="True" truevalue="-ignore_bad_data" type="boolean"/>
32 <param name="param_prob_correct" type="boolean" truevalue="-prob_correct true" falsevalue="-prob_correct false" 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)"/> 65 <param checked="false" falsevalue="" help="(-prob_correct) " label="If set scores will be calculated as '1 - ErrorProbabilities' and can be interpreted as probabilities for correct identifications" name="param_prob_correct" optional="True" truevalue="-prob_correct" type="boolean"/>
33 <expand macro="advanced_options"> 66 <expand macro="advanced_options">
34 <param name="param_smallest_e_value" type="float" value="1e-19" label="This value gives a lower bound to E-Values. It should not be 0, as transformation in a real number (log of E-value) is not possible for certain values then." help="(-smallest_e_value)"/> 67 <param 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" label="Only used, when top_hits_only set" name="param_fdr_for_targets_smaller" type="float" value="0.05"/>
35 <param name="param_fdr_for_targets_smaller" type="float" value="0.05" label="Only used, when top_hits_only set. Additionally, target_decoy information should be available. The score_type must be q-value from an previous False Discovery Rate run." help="(-fdr_for_targets_smaller)"/> 68 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
36 <param name="param_number_of_bins" type="integer" value="100" label="Number of bins used for visualization. Only needed if each iteration step of the EM-Algorithm will be visualized" help="(-number_of_bins)"/> 69 <param help="(-number_of_bins) Only needed if each iteration step of the EM-Algorithm will be visualized" label="Number of bins used for visualization" name="param_fit_algorithm_number_of_bins" type="integer" value="100"/>
37 <param name="param_incorrectly_assigned" type="select" optional="True" value="Gumbel" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences. For 'Gauss', the Gauss distribution is used." help="(-incorrectly_assigned)"> 70 <param help="(-incorrectly_assigned) For 'Gauss', the Gauss distribution is used" label="for 'Gumbel', the Gumbel distribution is used to plot incorrectly assigned sequences" name="param_fit_algorithm_incorrectly_assigned" optional="True" type="select" value="Gumbel">
38 <option value="Gumbel">Gumbel</option> 71 <option value="Gumbel">Gumbel</option>
39 <option value="Gauss">Gauss</option> 72 <option value="Gauss">Gauss</option>
40 </param> 73 </param>
41 </expand> 74 <param help="(-max_nr_iterations) " label="Bounds the number of iterations for the EM algorithm when convergence is slow" name="param_fit_algorithm_max_nr_iterations" type="integer" value="1000"/>
42 </inputs> 75 </expand>
43 <outputs> 76 </inputs>
44 <data name="param_out" label="output file " format="idXML"/> 77 <outputs>
45 <data name="param_out_plot" label="txt file (if gnuplot is available, a corresponding PDF will be created as well.)" format="txt"/> 78 <data format="xml" name="param_out"/>
46 </outputs> 79 <data format="txt" name="param_out_plot"/>
47 <help>**What it does** 80 </outputs>
48 81 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
49 Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
50 82
51 83
52 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html 84 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help>
53 85 </tool>
54 @REFERENCES@
55 </help>
56 </tool>