Mercurial > repos > galaxyp > openms_rtpredict

annotate RTPredict.xml @ 1:ad805b03ddf8 draft

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author galaxyp
date Wed, 09 Aug 2017 09:55:48 -0400
parents 44f9dcfd2542
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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: [Peptide property prediction]-->
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4 <tool id="RTPredict" name="RTPredict" version="2.2.0">
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5 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RTPredict</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>RTPredict
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14
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15 #if $param_in_id:
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16 -in_id $param_in_id
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17 #end if
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18 #if $param_in_text:
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19 -in_text $param_in_text
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20 #end if
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21 #if $param_in_oligo_params:
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22 -in_oligo_params $param_in_oligo_params
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23 #end if
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24 #if $param_in_oligo_trainset:
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25 -in_oligo_trainset $param_in_oligo_trainset
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26 #end if
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27 #if $param_svm_model:
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28 -svm_model $param_svm_model
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29 #end if
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30 #if $param_total_gradient_time:
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31 -total_gradient_time $param_total_gradient_time
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32 #end if
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33 #if $param_out_id_file:
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34 -out_id:file $param_out_id_file
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35 #end if
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36 #if $param_out_id_positive:
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37 -out_id:positive $param_out_id_positive
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38 #end if
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39 #if $param_out_id_negative:
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40 -out_id:negative $param_out_id_negative
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41 #end if
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42 #if $param_out_text_file:
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43 -out_text:file $param_out_text_file
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44 #end if
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45 #if $adv_opts.adv_opts_selector=='advanced':
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46 #if $adv_opts.param_max_number_of_peptides:
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47 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
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48 #end if
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
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53 -out_id:rewrite_peptideidentification_rtmz
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54 #end if
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55 #end if
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56 </command>
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57 <inputs>
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58 <param name="param_in_id" type="data" format="idxml" optional="True" label="Peptides with precursor information" help="(-in_id) "/>
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59 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text) "/>
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60 <param name="param_in_oligo_params" type="data" format="paramXML" optional="True" label="input file with additional model parameters when using the OLIGO kernel" help="(-in_oligo_params) "/>
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61 <param name="param_in_oligo_trainset" type="data" format="txt" optional="True" label="input file with the used training dataset when using the OLIGO kernel" help="(-in_oligo_trainset) "/>
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62 <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model) "/>
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63 <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time) "/>
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64 <expand macro="advanced_options">
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65 <param name="param_max_number_of_peptides" type="integer" value="100000" label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" help="(-max_number_of_peptides) "/>
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66 <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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67 <param name="param_out_id_rewrite_peptideidentification_rtmz" display="radio" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz" falsevalue="" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz) "/>
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68 </expand>
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69 </inputs>
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70 <outputs>
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71 <data name="param_out_id_file" format="idxml"/>
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72 <data name="param_out_id_positive" format="idxml"/>
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73 <data name="param_out_id_negative" format="idxml"/>
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74 <data name="param_out_text_file" format="tabular"/>
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75 </outputs>
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76 <help>Predicts retention times for peptides using a model trained by RTModel.
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77
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78
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79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
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80 </tool>