Mercurial > repos > galaxyp > openms_idposteriorerrorprobability

comparison IDPosteriorErrorProbability.xml @ 12:e0bff01d89c0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:58:55 -0400
parents 0af4f030fb65
children dd366d7a206e
comparison
equal deleted inserted replaced
11:aa76d3d3e751 12:e0bff01d89c0
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 CTD2Galaxy.--> 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="2.2.0"> 4 <tool id="IDPosteriorErrorProbability" name="IDPosteriorErrorProbability" version="2.3.0">
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 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IDPosteriorErrorProbability 13 <command detect_errors="aggressive"><![CDATA[IDPosteriorErrorProbability
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
53 #end if 53 #end if
54 #if $adv_opts.param_fit_algorithm_max_nr_iterations: 54 #if $adv_opts.param_fit_algorithm_max_nr_iterations:
55 -fit_algorithm:max_nr_iterations $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 56 #end if
57 #end if 57 #end if
58 </command> 58 ]]></command>
59 <inputs> 59 <inputs>
60 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/> 60 <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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"/> 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"/>
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) "/> 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) "/>
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"/> 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"/>
78 <data name="param_out_plot" format="txt"/> 78 <data name="param_out_plot" format="txt"/>
79 </outputs> 79 </outputs>
80 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 80 <help>Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model.
81 81
82 82
83 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDPosteriorErrorProbability.html</help> 83 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDPosteriorErrorProbability.html</help>
84 </tool> 84 </tool>