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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RTPredict" name="RTPredict" version="2.0.0">
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3 <description>Predicts retention times for peptides using a model trained by RTModel.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">RTPredict</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>RTPredict
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11
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12 #if $param_in_id:
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13 -in_id $param_in_id
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14 #end if
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15 #if $param_in_text:
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16 -in_text $param_in_text
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17 #end if
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18 #if $param_svm_model:
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19 -svm_model $param_svm_model
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20 #end if
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21 #if $param_total_gradient_time:
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22 -total_gradient_time $param_total_gradient_time
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23 #end if
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24 -threads \${GALAXY_SLOTS:-24}
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25 #if $param_out_id_file:
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26 -out_id:file $param_out_id_file
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27 #end if
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28 #if $param_out_id_positive:
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29 -out_id:positive $param_out_id_positive
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30 #end if
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31 #if $param_out_id_negative:
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32 -out_id:negative $param_out_id_negative
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33 #end if
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34 #if $param_out_text_file:
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35 -out_text:file $param_out_text_file
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36 #end if
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37 #if $adv_opts.adv_opts_selector=='advanced':
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38 #if $adv_opts.param_max_number_of_peptides:
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39 -max_number_of_peptides $adv_opts.param_max_number_of_peptides
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40 #end if
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
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45 -out_id:rewrite_peptideidentification_rtmz
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46 #end if
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47 #end if
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48 </command>
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49 <inputs>
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50 <param name="param_in_id" type="data" format="idxml" optional="True" label="Peptides with precursor information" help="(-in_id) "/>
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51 <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text) "/>
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52 <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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53 <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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54 <expand macro="advanced_options">
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55 <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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56 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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57 <param name="param_out_id_rewrite_peptideidentification_rtmz" 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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58 </expand>
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59 </inputs>
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60 <outputs>
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61 <data name="param_out_id_file" format="idxml"/>
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62 <data name="param_out_id_positive" format="idxml"/>
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63 <data name="param_out_id_negative" format="idxml"/>
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64 <data name="param_out_text_file" format="tabular"/>
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65 </outputs>
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66 <help>**What it does**
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67
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68 Predicts retention times for peptides using a model trained by RTModel.
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69
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70
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71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html</help>
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72 <expand macro="references"/>
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73 </tool>
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