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comparison cherri_train.xml @ 3:a30b9df1775a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit 8778c3f71e295ec5b62ef3998319d211fc864e35
author iuc
date Wed, 25 Jan 2023 18:33:19 +0000
parents ed0efb924438
children
comparison
equal deleted inserted replaced
2:ed0efb924438 3:a30b9df1775a
1 <tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@" profile="@PROFILE@"> 1 <tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements"/> 5 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 export PYTHONHASHSEED=31337 && 7 export PYTHONHASHSEED=31337 &&
8 mkdir mixed_model &&
9 #set experiments = [] 8 #set experiments = []
10 #for $experiment in $rep_experiment: 9 #for $experiment in $rep_experiment:
11 mkdir $experiment.exp_name && 10 mkdir $experiment.exp_name &&
11 mkdir '$experiment.exp_name/tmp' &&
12 ln -s '$experiment.ref_source.genome_fasta' '$experiment.exp_name/genome.fa' && 12 ln -s '$experiment.ref_source.genome_fasta' '$experiment.exp_name/genome.fa' &&
13 $experiments.append(str($experiment.exp_name)) 13 $experiments.append(str($experiment.exp_name))
14 #set replicates = [] 14 #set replicates = []
15 #for $i, $sample in enumerate($experiment.rep_samples): 15 #for $i, $sample in enumerate($experiment.rep_samples):
16 ln -s '$sample.file' '$experiment.exp_name/${i}.tabular' && 16 ln -s '$sample.file' '$experiment.exp_name/${i}.tabular' &&
24 -n '$experiment.exp_name' 24 -n '$experiment.exp_name'
25 #if $experiment.occupied_regions: 25 #if $experiment.occupied_regions:
26 -i2 '$experiment.occupied_regions' 26 -i2 '$experiment.occupied_regions'
27 #end if 27 #end if
28 -o . 28 -o .
29 -on '$experiment.exp_name' 29 -on '$experiment.exp_name'
30 -tp '$experiment.exp_name/tmp'
30 @COMMONPARAMS@ && 31 @COMMONPARAMS@ &&
31 #if len($rep_experiment) > 1: 32 #if len($rep_experiment) > 1:
33 mkdir -p mixed_model &&
32 ln -s '../$experiment.exp_name' 'mixed_model/$experiment.exp_name' && 34 ln -s '../$experiment.exp_name' 'mixed_model/$experiment.exp_name' &&
33 #else: 35 #else:
34 ln -s $experiment.exp_name/model/optimized/full_${experiment.exp_name}_context_${context}.model final_full.model && 36 ln -s $experiment.exp_name/model/optimized/full_${experiment.exp_name}_context_${context}.model final_full.model &&
35 #if $use_structure == 'off': 37 #if $use_structure == 'off':
36 ln -s $experiment.exp_name/model/features/${experiment.exp_name}_context_${context}.npz features.npz && 38 ln -s $experiment.exp_name/model/features/${experiment.exp_name}_context_${context}.npz features.npz &&
38 ln -s $experiment.exp_name/feature_files/training_data_${experiment.exp_name}_context_${context}.npz features.npz && 40 ln -s $experiment.exp_name/feature_files/training_data_${experiment.exp_name}_context_${context}.npz features.npz &&
39 #end if 41 #end if
40 #end if 42 #end if
41 #end for 43 #end for
42 #if len($rep_experiment) > 1: 44 #if len($rep_experiment) > 1:
45 mkdir mixed_model/tmp &&
43 cherri train 46 cherri train
44 -mi on 47 -mi on
45 -i1 mixed_model 48 -i1 mixed_model
46 -r #echo ' '.join($experiments) 49 -r #echo ' '.join($experiments)
47 -g /not/needed/ 50 -g /not/needed/
48 -l /not/needed/ 51 -l /not/needed/
49 -n mixed 52 -n mixed
50 -o . 53 -o .
51 -on mixed_model 54 -on mixed_model
55 -tp mixed_model/tmp
52 @COMMONPARAMS@ && 56 @COMMONPARAMS@ &&
53 ln -s mixed_model/mixed/model/optimized/full_mixed_context_${context}.model final_full.model && 57 ln -s mixed_model/mixed/model/optimized/full_mixed_context_${context}.model final_full.model &&
54 #if $use_structure == 'off': 58 #if $use_structure == 'off':
55 ln -s mixed_model/mixed/model/features/mixed_context_${context}.npz features.npz && 59 ln -s mixed_model/mixed/model/features/mixed_context_${context}.npz features.npz &&
56 #else: 60 #else: