Mercurial > repos > galaxyp > openms_iddecoyprobability

comparison IDDecoyProbability.xml @ 0:d85a484393b5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:50:18 -0500
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-1:000000000000 0:d85a484393b5
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="IDDecoyProbability" name="IDDecoyProbability" version="2.1.0">
5 <description>Estimates peptide probabilities using a decoy search strategy.
6 WARNING: This util is deprecated.</description>
7 <macros>
8 <token name="@EXECUTABLE@">IDDecoyProbability</token>
9 <import>macros.xml</import>
10 </macros>
11 <expand macro="references"/>
12 <expand macro="stdio"/>
13 <expand macro="requirements"/>
14 <command>IDDecoyProbability
15
16 #if $param_in:
17 -in $param_in
18 #end if
19 #if $param_fwd_in:
20 -fwd_in $param_fwd_in
21 #end if
22 #if $param_rev_in:
23 -rev_in $param_rev_in
24 #end if
25 #if $param_out:
26 -out $param_out
27 #end if
28 #if $adv_opts.adv_opts_selector=='advanced':
29 #if $adv_opts.param_force:
30 -force
31 #end if
32 #if $adv_opts.param_decoy_algorithm_number_of_bins:
33 -decoy_algorithm:number_of_bins $adv_opts.param_decoy_algorithm_number_of_bins
34 #end if
35 #if $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero:
36 -decoy_algorithm:lower_score_better_default_value_if_zero $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero
37 #end if
38 #end if
39 </command>
40 <inputs>
41 <param name="param_in" type="data" format="idxml" optional="True" label="Identification input of combined forward decoy search (reindex with PeptideIndexer first)" help="(-in) "/>
42 <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input of forward run" help="(-fwd_in) "/>
43 <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input of decoy run" help="(-rev_in) "/>
44 <expand macro="advanced_options">
45 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
46 <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) "/>
47 <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)"/>
48 </expand>
49 </inputs>
50 <outputs>
51 <data name="param_out" format="idxml"/>
52 </outputs>
53 <help>Estimates peptide probabilities using a decoy search strategy.
54 WARNING: This util is deprecated.
55
56
57 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html</help>
58 </tool>