Mercurial > repos > galaxyp > openms_iddecoyprobability

annotate IDDecoyProbability.xml @ 0:99effccd5e83 draft

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author galaxyp
date Wed, 01 Mar 2017 10:15:23 -0500
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99effccd5e83 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="IDDecoyProbability" name="IDDecoyProbability" version="2.1.0">
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5 <description>Estimates peptide probabilities using a decoy search strategy.
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6 WARNING: This util is deprecated.</description>
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7 <macros>
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8 <token name="@EXECUTABLE@">IDDecoyProbability</token>
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9 <import>macros.xml</import>
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10 </macros>
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11 <expand macro="references"/>
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12 <expand macro="stdio"/>
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13 <expand macro="requirements"/>
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14 <command>IDDecoyProbability
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15
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16 #if $param_in:
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17 -in $param_in
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18 #end if
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19 #if $param_fwd_in:
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20 -fwd_in $param_fwd_in
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21 #end if
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22 #if $param_rev_in:
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23 -rev_in $param_rev_in
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24 #end if
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25 #if $param_out:
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26 -out $param_out
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27 #end if
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28 #if $adv_opts.adv_opts_selector=='advanced':
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29 #if $adv_opts.param_force:
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30 -force
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31 #end if
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32 #if $adv_opts.param_decoy_algorithm_number_of_bins:
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33 -decoy_algorithm:number_of_bins $adv_opts.param_decoy_algorithm_number_of_bins
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34 #end if
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35 #if $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero:
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36 -decoy_algorithm:lower_score_better_default_value_if_zero $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero
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37 #end if
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38 #end if
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39 </command>
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40 <inputs>
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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) "/>
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42 <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input of forward run" help="(-fwd_in) "/>
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43 <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input of decoy run" help="(-rev_in) "/>
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44 <expand macro="advanced_options">
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45 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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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) "/>
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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)"/>
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data name="param_out" format="idxml"/>
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52 </outputs>
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53 <help>Estimates peptide probabilities using a decoy search strategy.
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54 WARNING: This util is deprecated.
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55
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56
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57 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html</help>
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58 </tool>