Mercurial > repos > iuc > cherri_train

annotate cherri_train.xml @ 2:ed0efb924438 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit b41099e2c6d73234688a07afdacb7c45e9de7575
author iuc
date Mon, 09 Jan 2023 19:50:32 +0000
parents f28df61581f4
children a30b9df1775a
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f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
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1 <tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@" profile="@PROFILE@">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
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2 <macros>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
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3 <import>macros.xml</import>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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4 </macros>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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5 <expand macro="requirements"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
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6 <command detect_errors="exit_code"><![CDATA[
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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7 export PYTHONHASHSEED=31337 &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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8 mkdir mixed_model &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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9 #set experiments = []
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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10 #for $experiment in $rep_experiment:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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11 mkdir $experiment.exp_name &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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12 ln -s '$experiment.ref_source.genome_fasta' '$experiment.exp_name/genome.fa' &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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13 $experiments.append(str($experiment.exp_name))
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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14 #set replicates = []
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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15 #for $i, $sample in enumerate($experiment.rep_samples):
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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16 ln -s '$sample.file' '$experiment.exp_name/${i}.tabular' &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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17 $replicates.append(str($i) + ".tabular")
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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18 #end for
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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19 cherri train
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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20 -i1 '$experiment.exp_name'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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21 -r #echo ' '.join($replicates)
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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22 -g '$experiment.exp_name/genome.fa'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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23 -l '$experiment.chrom_len_file'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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24 -n '$experiment.exp_name'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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25 #if $experiment.occupied_regions:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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26 -i2 '$experiment.occupied_regions'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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27 #end if
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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28 -o .
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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29 -on '$experiment.exp_name'
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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30 @COMMONPARAMS@ &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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31 #if len($rep_experiment) > 1:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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32 ln -s '../$experiment.exp_name' 'mixed_model/$experiment.exp_name' &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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33 #else:
2
ed0efb924438 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit b41099e2c6d73234688a07afdacb7c45e9de7575
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34 ln -s $experiment.exp_name/model/optimized/full_${experiment.exp_name}_context_${context}.model final_full.model &&
0
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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35 #if $use_structure == 'off':
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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36 ln -s $experiment.exp_name/model/features/${experiment.exp_name}_context_${context}.npz features.npz &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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37 #else:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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38 ln -s $experiment.exp_name/feature_files/training_data_${experiment.exp_name}_context_${context}.npz features.npz &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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39 #end if
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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40 #end if
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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41 #end for
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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42 #if len($rep_experiment) > 1:
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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43 cherri train
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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44 -mi on
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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45 -i1 mixed_model
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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46 -r #echo ' '.join($experiments)
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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47 -g /not/needed/
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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48 -l /not/needed/
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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49 -n mixed
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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50 -o .
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51 -on mixed_model
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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52 @COMMONPARAMS@ &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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53 ln -s mixed_model/mixed/model/optimized/full_mixed_context_${context}.model final_full.model &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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54 #if $use_structure == 'off':
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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55 ln -s mixed_model/mixed/model/features/mixed_context_${context}.npz features.npz &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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56 #else:
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57 ln -s mixed_model/mixed/feature_files/training_data_mixed_context_${context}.npz features.npz &&
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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58 #end if
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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59 #end if
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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60 tar -zhcvf model.tgz final_full.model features.npz
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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61 ]]></command>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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62 <inputs>
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63 <repeat name="rep_experiment" title="Experiment" min="1" default="1">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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64 <param name="exp_name" type="text" value="myExperiment" label="Name of the experiment" help="Only letters, numbers and underscores will be retained in this field. If more than one experiment is provided, then the tool generates a mixed model by combining datasets.">
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65 <sanitizer>
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66 <valid initial="string.letters,string.digits"><add value="_" /></valid>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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67 </sanitizer>
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68 </param>
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69 <expand macro="reference_source_conditional"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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70 <repeat name="rep_samples" title="Interaction summary file" min="1" default="1">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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71 <param name="file" type="data" format="tabular" multiple="false" label="Interaction summary file of a replicate" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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72 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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73 <param name="occupied_regions" optional="True" type="data" format="bed" label="Path to the genomic RBP crosslink or binding site locations (in BED format)" />
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74 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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75 <param name="context" type="integer" value="150" label="How much context should be added at up- and downstream of each sequence" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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76 <param name="intarna_param_file" optional="True" type="data" format="txt" label="IntaRNA parameters file" />
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77 <param name="use_structure" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Set 'off' if you want to disable structure, default 'on'" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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78 <param name="run_time" type="integer" value="43200" label="Time used for the optimization in seconds, default: 43200 (12h)" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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79 <param name="filter_hybrid" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Filter the data for hybrids already detected by ChiRA" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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80 </inputs>
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81 <outputs>
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82 <data name="out_model" format="tgz" from_work_dir="model.tgz" label="Trained model and features file on ${on_string}"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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83 </outputs>
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84 <tests>
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85 <!-- Single experiment -st on -->
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86 <test>
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87 <repeat name="rep_experiment">
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88 <param name="exp_name" value="myExperiment1"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
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89 <conditional name="ref_source">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
90 <param name="ref_source_selector" value="history"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
91 <param name="genome_fasta" value="train_1.fa"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
92 </conditional>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
93 <param name="chrom_len_file" value="train_2_len.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
94 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
95 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
96 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
97 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
98 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
99 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
100 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
101 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
102 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
103 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
104 <param name="run_time" value="60" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
105 <output name="out_model">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
106 <assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
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107 <has_size min="100000"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
108 </assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
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109 </output>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
110 </test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
111 <!-- Single experiment -st off -->
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
112 <test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
113 <repeat name="rep_experiment">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
114 <param name="exp_name" value="myExperiment1"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
115 <conditional name="ref_source">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
116 <param name="ref_source_selector" value="history"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
117 <param name="genome_fasta" value="train_1.fa"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
118 </conditional>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
119 <param name="chrom_len_file" value="train_2_len.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
120 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
121 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
122 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
123 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
124 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
125 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
126 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
127 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
128 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
129 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
130 <param name="run_time" value="60" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
131 <param name="use_structure" value="off" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
132 <output name="out_model">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
133 <assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
134 <has_size min="100000"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
135 </assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
136 </output>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
137 </test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
138 <!-- Mixed model -st on -->
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
139 <test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
140 <repeat name="rep_experiment">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
141 <param name="exp_name" value="myExperiment1"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
142 <conditional name="ref_source">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
143 <param name="ref_source_selector" value="history"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
144 <param name="genome_fasta" value="train_1.fa"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
145 </conditional>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
146 <param name="chrom_len_file" value="train_2_len.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
147 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
148 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
149 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
150 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
151 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
152 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
153 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
154 <param name="file" value="train_1_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
155 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
156 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
157 <repeat name="rep_experiment">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
158 <param name="exp_name" value="myExperiment2"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
159 <conditional name="ref_source">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
160 <param name="ref_source_selector" value="history"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
161 <param name="genome_fasta" value="train_2.fa"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
162 </conditional>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
163 <param name="chrom_len_file" value="train_2_len.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
164 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
165 <param name="file" value="train_2_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
166 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
167 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
168 <param name="file" value="train_2_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
169 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
170 <repeat name="rep_samples">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
171 <param name="file" value="train_2_pos.tabular" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
172 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
173 </repeat>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
174 <param name="run_time" value="60" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
175 <param name="context" value="100" />
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
176 <output name="out_model">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
177 <assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
178 <has_size min="100000"/>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
179 </assert_contents>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
180 </output>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
181 </test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
182 <!-- Mixed model -st off -->
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
183 <test>
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
parents:
diff changeset
184 <repeat name="rep_experiment">
f28df61581f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
iuc
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185 <param name="exp_name" value="myExperiment1"/>
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186 <conditional name="ref_source">
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187 <param name="ref_source_selector" value="history"/>
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188 <param name="genome_fasta" value="train_1.fa"/>
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189 </conditional>
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190 <param name="chrom_len_file" value="train_2_len.tabular" />
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191 <repeat name="rep_samples">
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192 <param name="file" value="train_1_pos.tabular" />
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193 </repeat>
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194 <repeat name="rep_samples">
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195 <param name="file" value="train_1_pos.tabular" />
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196 </repeat>
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197 <repeat name="rep_samples">
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198 <param name="file" value="train_1_pos.tabular" />
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199 </repeat>
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200 </repeat>
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201 <repeat name="rep_experiment">
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202 <param name="exp_name" value="myExperiment2"/>
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203 <conditional name="ref_source">
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204 <param name="ref_source_selector" value="history"/>
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205 <param name="genome_fasta" value="train_2.fa"/>
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206 </conditional>
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207 <param name="chrom_len_file" value="train_2_len.tabular" />
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208 <repeat name="rep_samples">
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209 <param name="file" value="train_2_pos.tabular" />
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210 </repeat>
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211 <repeat name="rep_samples">
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212 <param name="file" value="train_2_pos.tabular" />
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213 </repeat>
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214 <repeat name="rep_samples">
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215 <param name="file" value="train_2_pos.tabular" />
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216 </repeat>
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217 </repeat>
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218 <param name="run_time" value="60" />
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219 <param name="use_structure" value="off" />
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220 <output name="out_model">
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221 <assert_contents>
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222 <has_size min="100000"/>
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223 </assert_contents>
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224 </output>
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225 </test>
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226 </tests>
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227 <help><![CDATA[
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228 CheRRI in train mode to build a predictive model. Takes interactions summary files from ChiRA tool as input. Generates a model file and a features file that can be used in CheRRI eval mode.
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229 ]]></help>
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230 <expand macro="citations" />
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231 </tool>