Mercurial > repos > galaxyp > openms_iddecoyprobability
diff IDDecoyProbability.xml @ 0:d85a484393b5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author | galaxyp |
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date | Wed, 01 Mar 2017 12:50:18 -0500 (2017-03-01) |
parents | |
children | 05be207dc506 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IDDecoyProbability.xml Wed Mar 01 12:50:18 2017 -0500 @@ -0,0 +1,58 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Utilities]--> +<tool id="IDDecoyProbability" name="IDDecoyProbability" version="2.1.0"> + <description>Estimates peptide probabilities using a decoy search strategy. +WARNING: This util is deprecated.</description> + <macros> + <token name="@EXECUTABLE@">IDDecoyProbability</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>IDDecoyProbability + +#if $param_in: + -in $param_in +#end if +#if $param_fwd_in: + -fwd_in $param_fwd_in +#end if +#if $param_rev_in: + -rev_in $param_rev_in +#end if +#if $param_out: + -out $param_out +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_decoy_algorithm_number_of_bins: + -decoy_algorithm:number_of_bins $adv_opts.param_decoy_algorithm_number_of_bins +#end if + #if $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero: + -decoy_algorithm:lower_score_better_default_value_if_zero $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="idxml" optional="True" label="Identification input of combined forward decoy search (reindex with PeptideIndexer first)" help="(-in) "/> + <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input of forward run" help="(-fwd_in) "/> + <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input of decoy run" help="(-rev_in) "/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="param_decoy_algorithm_number_of_bins" type="integer" value="40" label="Number of bins used for the fitting, if sparse datasets are used, this number should be smalle" help="(-number_of_bins) "/> + <param name="param_decoy_algorithm_lower_score_better_default_value_if_zero" type="float" value="50.0" label="This value is used if" help="(-lower_score_better_default_value_if_zero) e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)"/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="idxml"/> + </outputs> + <help>Estimates peptide probabilities using a decoy search strategy. +WARNING: This util is deprecated. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html</help> +</tool>