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annotate RTPredict.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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="2.0.0">
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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_svm_model:
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22 -svm_model $param_svm_model
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23 #end if
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24 #if $param_total_gradient_time:
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25 -total_gradient_time $param_total_gradient_time
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26 #end if
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27 -threads \${GALAXY_SLOTS:-24}
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28 #if $param_out_id_file:
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29 -out_id:file $param_out_id_file
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30 #end if
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31 #if $param_out_id_positive:
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32 -out_id:positive $param_out_id_positive
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33 #end if
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34 #if $param_out_id_negative:
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35 -out_id:negative $param_out_id_negative
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36 #end if
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37 #if $param_out_text_file:
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38 -out_text:file $param_out_text_file
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39 #end if
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40 #if $adv_opts.adv_opts_selector=='advanced':
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41 #if $adv_opts.param_max_number_of_peptides:
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42 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
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43 #end if
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44 #if $adv_opts.param_force:
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45 -force
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46 #end if
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47 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
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48 -out_id:rewrite_peptideidentification_rtmz
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49 #end if
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50 #end if
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51 </command>
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52 <inputs>
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53 <param format="xml" help="(-in_id) " label="Peptides with precursor information" name="param_in_id" optional="True" type="data"/>
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54 <param format="txt" help="(-in_text) " label="Peptides as text-based file" name="param_in_text" optional="True" type="data"/>
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55 <param format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by RTModel)" name="param_svm_model" optional="False" type="data"/>
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56 <param help="(-total_gradient_time) " label="The time (in seconds) of the gradient (peptide RT prediction)" min="1e-05" name="param_total_gradient_time" optional="True" type="float" value="1.0"/>
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57 <expand macro="advanced_options">
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58 <param help="(-max_number_of_peptides) " label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
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59 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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60 <param checked="false" falsevalue="" help="(-rewrite_peptideidentification_rtmz) " label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" name="param_out_id_rewrite_peptideidentification_rtmz" optional="True" truevalue="-out_id:rewrite_peptideidentification_rtmz" type="boolean"/>
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61 </expand>
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62 </inputs>
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63 <outputs>
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64 <data format="xml" name="param_out_id_file"/>
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65 <data format="xml" name="param_out_id_positive"/>
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66 <data format="xml" name="param_out_id_negative"/>
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67 <data format="tabular" name="param_out_text_file"/>
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68 </outputs>
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69 <help>Predicts retention times for peptides using a model trained by RTModel.
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71
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72 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
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73 </tool>