flexynesis: flexynesis.xml annotate

author	bgruening
date	Mon, 12 Aug 2024 17:58:02 +0000
parents
children	b353dad17ab7

rev	line source
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	1 <tool id="flexynesis" name="Flexynesis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	2 <description>A deep-learning based multi-omics bulk sequencing data integration suite</description>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	3 <macros>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	4 <import>macros.xml</import>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	5 </macros>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	6 <expand macro="edam"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	7 <expand macro="requirements"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	9 @CHECK_NON_COMMERCIAL_USE@
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	10 mkdir -p input/test input/train output &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	11 ln -s '$train_clin' input/train/clin.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	12 ln -s '$test_clin' input/test/clin.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	13
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	14 #if str($assay_main) != '':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	15 #set $name = str($assay_main.replace(" ", "_"))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	16 ln -s '$train_omics_main' input/train/${name}.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	17 ln -s '$test_omics_main' input/test/${name}.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	18 #set $data_names = [$name]
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	19 #else
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	20 ln -s '$train_omics_main' input/train/main.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	21 ln -s '$test_omics_main' input/test/main.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	22 #set $data_names = ['main']
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	23 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	24 #if str($training_type.model) == 'cm_train':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	25 #if str($layer_main) == 'input':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	26 #set $input_layers = $data_names
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	27 #set $output_layers = []
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	28 #else
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	29 #set $input_layers = []
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	30 #set $output_layers = $data_names
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	31 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	32 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	33 #for $i, $element in enumerate($omics)
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	34 #if str($element.train_omics) != 'None' and str($element.test_omics) != 'None':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	35 #if str($element.assay) != '':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	36 #set $i = str($element.assay.replace(" ", "_"))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	37 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	38 ln -s '${element.train_omics}' input/train/omics_${i}.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	39 ln -s '${element.test_omics}' input/test/omics_${i}.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	40 $data_names.append("omics_" + str($i))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	41 #if str($training_type.model) == 'cm_train':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	42 #if str($element.layer) == 'input':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	43 $input_layers.append("omics_" + str($i))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	44 #else
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	45 $output_layers.append("omics_" + str($i))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	46 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	47 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	48 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	49 #end for
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	50 flexynesis
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	51 --data_path 'input'
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	52 --outdir 'output'
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	53 --model_class $model_class
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	54 #if str($model_class) == 'GNN':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	55 --gnn_conv_type $gnn_conv_type
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	56 --string_organism $string_organism
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	57 --string_node_name $string_node_name
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	58 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	59 #if str($training_type.model) == 's_train':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	60 #if str($target_variables) != '':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	61 --target_variables $target_variables
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	62 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	63 #if str($surv_event_var) != '':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	64 --surv_event_var $surv_event_var
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	65 --surv_time_var $surv_time_var
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	66 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	67 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	68 #if str($training_type.model) == 'cm_train':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	69 --input_layers $str(",".join($input_layers))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	70 --output_layers $str(",".join($output_layers))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	71 #end if
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	72 --fusion_type $fusion_type
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	73 --hpo_iter $hpo_iter
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	74 --finetuning_samples $finetuning_samples
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	75 --variance_threshold $variance_threshold
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	76 --correlation_threshold $correlation_threshold
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	77 --subsample $subsample
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	78 --features_min $features_min
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	79 --features_top_percentile $features_top_percentile
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	80 --data_types $str(",".join($data_names))
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	81 --early_stop_patience $early_stop_patience
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	82 --hpo_patience $hpo_patience
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	83 $log_transform
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	84 $use_loss_weighting
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	85 $use_cv
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	86 $evaluate_baseline_performance
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	87 $disable_marker_finding
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	88 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	89 ]]></command>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	90 <inputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	91 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	92 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	93 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	94 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	95 <param name="model" type="select" label="Type of Analysis" >
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	96 <option value="s_train">Supervised training</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	97 <option value="us_train">Unsupervised Training</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	98 <option value="cm_train">Cross-modality Training</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	99 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	100 <when value="s_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	101 <expand macro="main_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	102 <repeat name="omics" min="0" title="Multiple omics layers?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	103 <expand macro="extra_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	104 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	105 <conditional name="model_class" label="Model class">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	106 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	107 <option value="DirectPred">DirectPred</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	108 <option value="GNN">GNN</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	109 <option value="MultiTripletNetwork">MultiTripletNetwork</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	110 <option value="RandomForest">RandomForest</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	111 <option value="SVM">SVM</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	112 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	113 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	114 <when value="DirectPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	115 <when value="GNN">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	116 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	117 <option value="GC">GC</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	118 <option value="GCN">GCN</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	119 <option value="SAGE">SAGE</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	120 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	121 <param argument="--string_organism" type="select" label="STRING DB organism">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	122 <option value="9606">Homo sapiens</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	123 <option value="10090">Mus musculus</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	124 <option value="10116">Rattus norvegicus</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	125 <option value="9544">Macaca mulatta</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	126 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	127 <param argument="--string_node_name" type="select" label="String node name" >
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	128 <option value="gene_name">Gene name</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	129 <option value="gene_id">Gene id</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	130 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	131 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	132 <when value="MultiTripletNetwork"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	133 <when value="RandomForest"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	134 <when value="SVM"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	135 <when value="RandomSurvivalForest"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	136 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	137 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	138 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	139 <valid initial="string.printable"></valid>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	140 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	141 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	142 <param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	143 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	144 <valid initial="string.printable"></valid>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	145 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	146 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	147 <param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	148 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	149 <valid initial="string.printable"></valid>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	150 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	151 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	152 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	153 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	154 <when value="us_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	155 <expand macro="main_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	156 <repeat name="omics" min="0" title="Multiple omics layers?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	157 <expand macro="extra_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	158 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	159 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	160 <option value="supervised_vae">supervised_vae</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	161 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	162 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	163 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	164 <when value="cm_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	165 <expand macro="main_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	166 <param name="layer_main" type="select" label="Use this omics data as input or output layer?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	167 <option value="input">Input</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	168 <option value="output">output</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	169 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	170 <repeat name="omics" min="0" title="Multiple omics layers?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	171 <expand macro="extra_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	172 <param name="layer" type="select" label="Use this omics data as input or output layer?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	173 <option value="input">Input</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	174 <option value="output">output</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	175 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	176 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	177 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	178 <option value="CrossModalPred">CrossModalPred</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	179 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	180 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	181 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	182 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	183 </inputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	184 <outputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	185 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	186 <discover_datasets pattern="(?P<name>.+)\.csv$" format="csv" directory="output"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	187 </collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	188 </outputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	189 <tests>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	190 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	191 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	192 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	193 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	194 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	195 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	196 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	197 <repeat name="omics">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	198 <param name="train_omics" value="train/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	199 <param name="test_omics" value="test/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	200 <param name="assay" value="foo"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	201 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	202 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	203 <param name="model" value="s_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	204 <param name="model_class" value="DirectPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	205 <param name="target_variables" value="Erlotinib"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	206 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	207 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	208 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	209 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	210 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	211 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	212 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	213 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	214 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	215 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	216 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	217 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	218 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	219 <element name="job.feature_importance">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	220 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	221 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	222 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	223 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	224 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	225 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	226 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	227 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	228 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	229 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	230 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	231 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	232 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	233 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	234 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	235 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	236 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	237 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	238 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	239 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	240 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	241 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	242 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	243 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	244 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	245 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	246 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	247 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	248 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	249 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	250 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	251 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	252 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	253 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	254 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	255 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	256 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	257 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	258 <param name="model" value="s_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	259 <param name="model_class" value="DirectPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	260 <param name="target_variables" value="Erlotinib"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	261 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	262 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	263 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	264 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	265 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	266 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	267 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	268 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	269 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	270 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	271 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	272 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	273 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	274 <element name="job.feature_importance">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	275 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	276 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	277 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	278 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	279 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	280 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	281 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	282 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	283 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	284 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	285 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	286 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	287 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	288 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	289 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	290 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	291 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	292 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	293 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	294 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	295 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	296 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	297 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	298 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	299 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	300 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	301 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	302 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	303 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	304 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	305 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	306 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	307 <repeat name="omics">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	308 <param name="train_omics" value="train/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	309 <param name="test_omics" value="test/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	310 <param name="assay" value="foo"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	311 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	312 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	313 <param name="model" value="s_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	314 <param name="model_class" value="DirectPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	315 <param name="target_variables" value="Irinotecan"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	316 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	317 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	318 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	319 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	320 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	321 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	322 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	323 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	324 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	325 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	326 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	327 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	328 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	329 <element name="job.feature_importance">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	330 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	331 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	332 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	333 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	334 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	335 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	336 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	337 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	338 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	339 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	340 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	341 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	342 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	343 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	344 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	345 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	346 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	347 <has_text_matching expression="source_dataset:A-704,Irinotecan,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	348 <has_text_matching expression="target_dataset:KMRC-20,Irinotecan,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	349 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	350 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	351 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	352 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	353 <has_text_matching expression="DirectPred,Irinotecan,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	354 <has_text_matching expression="DirectPred,Irinotecan,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	355 <has_text_matching expression="DirectPred,Irinotecan,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	356 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	357 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	358 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	359 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	360 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	361 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	362 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	363 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	364 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	365 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	366 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	367 <repeat name="omics">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	368 <param name="train_omics" value="train/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	369 <param name="test_omics" value="test/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	370 <param name="assay" value="foo"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	371 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	372 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	373 <param name="model" value="us_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	374 <param name="model_class" value="supervised_vae"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	375 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	376 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	377 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	378 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	379 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	380 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	381 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	382 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	383 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	384 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	385 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	386 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	387 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	388 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	389 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	390 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	391 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	392 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	393 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	394 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	395 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	396 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	397 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	398 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	399 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	400 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	401 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	402 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	403 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	404 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	405 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	406 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	407 <param name="layer_main" value="input"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	408 <repeat name="omics">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	409 <param name="train_omics" value="train/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	410 <param name="test_omics" value="test/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	411 <param name="assay" value="foo"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	412 <param name="layer" value="output"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	413 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	414 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	415 <param name="model" value="cm_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	416 <param name="model_class" value="CrossModalPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	417 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	418 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	419 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	420 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	421 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	422 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	423 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	424 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	425 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	426 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	427 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	428 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	429 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	430 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	431 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	432 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	433 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	434 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	435 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	436 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	437 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	438 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	439 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	440 <element name="job.test_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	441 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	442 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	443 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	444 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	445 <element name="job.train_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	446 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	447 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	448 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	449 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	450 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	451 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	452 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	453 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	454 <param name="train_clin" value="train/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	455 <param name="test_clin" value="test/clin" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	456 <param name="train_omics_main" value="train/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	457 <param name="test_omics_main" value="test/gex" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	458 <param name="assay_main" value="bar"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	459 <repeat name="omics">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	460 <param name="train_omics" value="train/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	461 <param name="test_omics" value="test/cnv" ftype="csv"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	462 <param name="assay" value="foo"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	463 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	464 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	465 <param name="model" value="s_train"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	466 <param name="model_class" value="GNN"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	467 <param name="gnn_conv_type" value="GC"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	468 <param name="string_organism" value="9606"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	469 <param name="string_node_name" value="gene_name"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	470 <param name="target_variables" value="Erlotinib"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	471 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	472 <param name="hpo_iter" value="1"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	473 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	474 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	475 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	476 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	477 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	478 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	479 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	480 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	481 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	482 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	483 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	484 <element name="job.feature_importance">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	485 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	486 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	487 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	488 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	489 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	490 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	491 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	492 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	493 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	494 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	495 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	496 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	497 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	498 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	499 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	500 <element name="job.predicted_labels">

0

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1 <tool id="flexynesis" name="Flexynesis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

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2 <description>A deep-learning based multi-omics bulk sequencing data integration suite</description>

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3 <macros>

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4 <import>macros.xml</import>

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5 </macros>

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6 <expand macro="edam"/>

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7 <expand macro="requirements"/>

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8 <command detect_errors="exit_code"><![CDATA[

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9 @CHECK_NON_COMMERCIAL_USE@

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10 mkdir -p input/test input/train output &&

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11 ln -s '$train_clin' input/train/clin.csv &&

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12 ln -s '$test_clin' input/test/clin.csv &&

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13

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14 #if str($assay_main) != '':

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15 #set $name = str($assay_main.replace(" ", "_"))

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16 ln -s '$train_omics_main' input/train/${name}.csv &&

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17 ln -s '$test_omics_main' input/test/${name}.csv &&

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18 #set $data_names = [$name]

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19 #else

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20 ln -s '$train_omics_main' input/train/main.csv &&

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21 ln -s '$test_omics_main' input/test/main.csv &&

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22 #set $data_names = ['main']

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23 #end if

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24 #if str($training_type.model) == 'cm_train':

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25 #if str($layer_main) == 'input':

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26 #set $input_layers = $data_names

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27 #set $output_layers = []

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28 #else

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29 #set $input_layers = []

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30 #set $output_layers = $data_names

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31 #end if

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32 #end if

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33 #for $i, $element in enumerate($omics)

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34 #if str($element.train_omics) != 'None' and str($element.test_omics) != 'None':

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35 #if str($element.assay) != '':

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36 #set $i = str($element.assay.replace(" ", "_"))

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37 #end if

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38 ln -s '${element.train_omics}' input/train/omics_${i}.csv &&

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39 ln -s '${element.test_omics}' input/test/omics_${i}.csv &&

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40 $data_names.append("omics_" + str($i))

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41 #if str($training_type.model) == 'cm_train':

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42 #if str($element.layer) == 'input':

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43 $input_layers.append("omics_" + str($i))

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44 #else

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45 $output_layers.append("omics_" + str($i))

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46 #end if

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47 #end if

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48 #end if

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49 #end for

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50 flexynesis

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51 --data_path 'input'

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52 --outdir 'output'

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53 --model_class $model_class

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54 #if str($model_class) == 'GNN':

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55 --gnn_conv_type $gnn_conv_type

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56 --string_organism $string_organism

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57 --string_node_name $string_node_name

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58 #end if

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59 #if str($training_type.model) == 's_train':

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60 #if str($target_variables) != '':

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61 --target_variables $target_variables

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62 #end if

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63 #if str($surv_event_var) != '':

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64 --surv_event_var $surv_event_var

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65 --surv_time_var $surv_time_var

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66 #end if

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67 #end if

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68 #if str($training_type.model) == 'cm_train':

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69 --input_layers $str(",".join($input_layers))

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70 --output_layers $str(",".join($output_layers))

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71 #end if

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72 --fusion_type $fusion_type

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73 --hpo_iter $hpo_iter

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74 --finetuning_samples $finetuning_samples

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75 --variance_threshold $variance_threshold

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76 --correlation_threshold $correlation_threshold

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77 --subsample $subsample

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78 --features_min $features_min

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79 --features_top_percentile $features_top_percentile

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80 --data_types $str(",".join($data_names))

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81 --early_stop_patience $early_stop_patience

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82 --hpo_patience $hpo_patience

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83 $log_transform

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84 $use_loss_weighting

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85 $use_cv

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86 $evaluate_baseline_performance

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87 $disable_marker_finding

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88 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}

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89 ]]></command>

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90 <inputs>

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91 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">

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92 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>

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93 </param>

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94 <conditional name="training_type">

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95 <param name="model" type="select" label="Type of Analysis" >

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96 <option value="s_train">Supervised training</option>

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97 <option value="us_train">Unsupervised Training</option>

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98 <option value="cm_train">Cross-modality Training</option>

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99 </param>

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100 <when value="s_train">

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101 <expand macro="main_inputs"/>

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102 <repeat name="omics" min="0" title="Multiple omics layers?">

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103 <expand macro="extra_inputs"/>

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104 </repeat>

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105 <conditional name="model_class" label="Model class">

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106 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">

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107 <option value="DirectPred">DirectPred</option>

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108 <option value="GNN">GNN</option>

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109 <option value="MultiTripletNetwork">MultiTripletNetwork</option>

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110 <option value="RandomForest">RandomForest</option>

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111 <option value="SVM">SVM</option>

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112 <option value="RandomSurvivalForest">RandomSurvivalForest</option>

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113 </param>

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114 <when value="DirectPred"/>

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115 <when value="GNN">

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116 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">

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117 <option value="GC">GC</option>

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118 <option value="GCN">GCN</option>

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119 <option value="SAGE">SAGE</option>

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120 </param>

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121 <param argument="--string_organism" type="select" label="STRING DB organism">

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122 <option value="9606">Homo sapiens</option>

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123 <option value="10090">Mus musculus</option>

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124 <option value="10116">Rattus norvegicus</option>

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125 <option value="9544">Macaca mulatta</option>

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126 </param>

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127 <param argument="--string_node_name" type="select" label="String node name" >

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128 <option value="gene_name">Gene name</option>

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129 <option value="gene_id">Gene id</option>

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130 </param>

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131 </when>

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132 <when value="MultiTripletNetwork"/>

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133 <when value="RandomForest"/>

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134 <when value="SVM"/>

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135 <when value="RandomSurvivalForest"/>

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136 </conditional>

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137 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">

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138 <sanitizer invalid_char="">

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139 <valid initial="string.printable"></valid>

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140 </sanitizer>

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141 </param>

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142 <param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">

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143 <sanitizer invalid_char="">

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144 <valid initial="string.printable"></valid>

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145 </sanitizer>

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146 </param>

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147 <param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">

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148 <sanitizer invalid_char="">

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149 <valid initial="string.printable"></valid>

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150 </sanitizer>

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151 </param>

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152 <expand macro="advanced"/>

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153 </when>

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154 <when value="us_train">

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155 <expand macro="main_inputs"/>

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156 <repeat name="omics" min="0" title="Multiple omics layers?">

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157 <expand macro="extra_inputs"/>

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158 </repeat>

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159 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">

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160 <option value="supervised_vae">supervised_vae</option>

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161 </param>

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162 <expand macro="advanced"/>

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163 </when>

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164 <when value="cm_train">

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165 <expand macro="main_inputs"/>

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166 <param name="layer_main" type="select" label="Use this omics data as input or output layer?">

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167 <option value="input">Input</option>

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168 <option value="output">output</option>

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169 </param>

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170 <repeat name="omics" min="0" title="Multiple omics layers?">

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171 <expand macro="extra_inputs"/>

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172 <param name="layer" type="select" label="Use this omics data as input or output layer?">

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173 <option value="input">Input</option>

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174 <option value="output">output</option>

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175 </param>

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176 </repeat>

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177 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">

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178 <option value="CrossModalPred">CrossModalPred</option>

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179 </param>

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180 <expand macro="advanced"/>

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181 </when>

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182 </conditional>

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183 </inputs>

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184 <outputs>

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185 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">

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186 <discover_datasets pattern="(?P<name>.+)\.csv$" format="csv" directory="output"/>

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187 </collection>

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188 </outputs>

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189 <tests>

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190 <test>

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191 <param name="non_commercial_use" value="True"/>

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192 <param name="train_clin" value="train/clin" ftype="csv"/>

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193 <param name="test_clin" value="test/clin" ftype="csv"/>

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194 <param name="train_omics_main" value="train/gex" ftype="csv"/>

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195 <param name="test_omics_main" value="test/gex" ftype="csv"/>

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196 <param name="assay_main" value="bar"/>

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197 <repeat name="omics">

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198 <param name="train_omics" value="train/cnv" ftype="csv"/>

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199 <param name="test_omics" value="test/cnv" ftype="csv"/>

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200 <param name="assay" value="foo"/>

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201 </repeat>

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202 <conditional name="training_type">

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203 <param name="model" value="s_train"/>

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204 <param name="model_class" value="DirectPred"/>

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205 <param name="target_variables" value="Erlotinib"/>

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206 </conditional>

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207 <param name="hpo_iter" value="1"/>

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208 <output_collection name="results" type="list">

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209 <element name="job.embeddings_test">

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210 <assert_contents>

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211 <has_n_lines n="50"/>

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212 </assert_contents>

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213 </element>

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214 <element name="job.embeddings_train">

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215 <assert_contents>

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216 <has_n_lines n="50"/>

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217 </assert_contents>

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218 </element>

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219 <element name="job.feature_importance">

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220 <assert_contents>

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221 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>

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222 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>

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223 </assert_contents>

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224 </element>

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225 <element name="job.feature_logs.bar">

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226 <assert_contents>

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227 <has_n_lines n="25"/>

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228 </assert_contents>

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229 </element>

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230 <element name="job.feature_logs.omics_foo">

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231 <assert_contents>

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232 <has_n_lines n="25"/>

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233 </assert_contents>

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234 </element>

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235 <element name="job.predicted_labels">

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236 <assert_contents>

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237 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>

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238 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>

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239 </assert_contents>

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240 </element>

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241 <element name="job.stats">

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242 <assert_contents>

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243 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>

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244 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>

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245 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>

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246 </assert_contents>

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247 </element>

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248 </output_collection>

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249 </test>

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250 <test>

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251 <param name="non_commercial_use" value="True"/>

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252 <param name="train_clin" value="train/clin" ftype="csv"/>

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253 <param name="test_clin" value="test/clin" ftype="csv"/>

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254 <param name="train_omics_main" value="train/gex" ftype="csv"/>

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255 <param name="test_omics_main" value="test/gex" ftype="csv"/>

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256 <param name="assay_main" value="bar"/>

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257 <conditional name="training_type">

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258 <param name="model" value="s_train"/>

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259 <param name="model_class" value="DirectPred"/>

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260 <param name="target_variables" value="Erlotinib"/>

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261 </conditional>

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262 <param name="hpo_iter" value="1"/>

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263 <output_collection name="results" type="list">

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264 <element name="job.embeddings_test">

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265 <assert_contents>

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266 <has_n_lines n="50"/>

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267 </assert_contents>

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268 </element>

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269 <element name="job.embeddings_train">

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270 <assert_contents>

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271 <has_n_lines n="50"/>

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272 </assert_contents>

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273 </element>

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274 <element name="job.feature_importance">

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275 <assert_contents>

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276 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>

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277 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>

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278 </assert_contents>

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279 </element>

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280 <element name="job.feature_logs.bar">

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281 <assert_contents>

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282 <has_n_lines n="25"/>

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283 </assert_contents>

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284 </element>

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285 <element name="job.predicted_labels">

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286 <assert_contents>

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287 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>

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288 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>

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289 </assert_contents>

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290 </element>

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291 <element name="job.stats">

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292 <assert_contents>

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293 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>

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294 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>

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295 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>

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296 </assert_contents>

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297 </element>

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298 </output_collection>

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299 </test>

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300 <test>

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301 <param name="non_commercial_use" value="True"/>

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302 <param name="train_clin" value="train/clin" ftype="csv"/>

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303 <param name="test_clin" value="test/clin" ftype="csv"/>

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304 <param name="train_omics_main" value="train/gex" ftype="csv"/>

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305 <param name="test_omics_main" value="test/gex" ftype="csv"/>

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306 <param name="assay_main" value="bar"/>

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307 <repeat name="omics">

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308 <param name="train_omics" value="train/cnv" ftype="csv"/>

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309 <param name="test_omics" value="test/cnv" ftype="csv"/>

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310 <param name="assay" value="foo"/>

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311 </repeat>

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312 <conditional name="training_type">

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313 <param name="model" value="s_train"/>

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314 <param name="model_class" value="DirectPred"/>

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315 <param name="target_variables" value="Irinotecan"/>

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316 </conditional>

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317 <param name="hpo_iter" value="1"/>

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318 <output_collection name="results" type="list">

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319 <element name="job.embeddings_test">

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320 <assert_contents>

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321 <has_n_lines n="50"/>

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322 </assert_contents>

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323 </element>

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324 <element name="job.embeddings_train">

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325 <assert_contents>

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326 <has_n_lines n="50"/>

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327 </assert_contents>

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328 </element>

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329 <element name="job.feature_importance">

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330 <assert_contents>

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331 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>

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332 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>

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333 </assert_contents>

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334 </element>

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335 <element name="job.feature_logs.bar">

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336 <assert_contents>

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337 <has_n_lines n="25"/>

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338 </assert_contents>

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339 </element>

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340 <element name="job.feature_logs.bar">

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341 <assert_contents>

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342 <has_n_lines n="25"/>

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343 </assert_contents>

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344 </element>

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345 <element name="job.predicted_labels">

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346 <assert_contents>

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347 <has_text_matching expression="source_dataset:A-704,Irinotecan,"/>

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348 <has_text_matching expression="target_dataset:KMRC-20,Irinotecan,"/>

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349 </assert_contents>

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350 </element>

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351 <element name="job.stats">

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352 <assert_contents>

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353 <has_text_matching expression="DirectPred,Irinotecan,numerical,mse,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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354 <has_text_matching expression="DirectPred,Irinotecan,numerical,r2,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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355 <has_text_matching expression="DirectPred,Irinotecan,numerical,pearson_corr,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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356 </assert_contents>

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357 </element>

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358 </output_collection>

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359 </test>

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360 <test>

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361 <param name="non_commercial_use" value="True"/>

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362 <param name="train_clin" value="train/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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363 <param name="test_clin" value="test/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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364 <param name="train_omics_main" value="train/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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365 <param name="test_omics_main" value="test/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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366 <param name="assay_main" value="bar"/>

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367 <repeat name="omics">

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368 <param name="train_omics" value="train/cnv" ftype="csv"/>

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369 <param name="test_omics" value="test/cnv" ftype="csv"/>

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370 <param name="assay" value="foo"/>

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371 </repeat>

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372 <conditional name="training_type">

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373 <param name="model" value="us_train"/>

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374 <param name="model_class" value="supervised_vae"/>

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375 </conditional>

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376 <param name="hpo_iter" value="1"/>

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377 <output_collection name="results" type="list">

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378 <element name="job.embeddings_test">

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379 <assert_contents>

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380 <has_n_lines n="50"/>

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381 </assert_contents>

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382 </element>

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383 <element name="job.embeddings_train">

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384 <assert_contents>

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385 <has_n_lines n="50"/>

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386 </assert_contents>

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387 </element>

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388 <element name="job.feature_logs.bar">

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389 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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390 <has_n_lines n="25"/>

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391 </assert_contents>

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392 </element>

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393 <element name="job.feature_logs.omics_foo">

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394 <assert_contents>

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395 <has_n_lines n="25"/>

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396 </assert_contents>

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397 </element>

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398 </output_collection>

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399 </test>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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400 <test>

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401 <param name="non_commercial_use" value="True"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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402 <param name="train_clin" value="train/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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403 <param name="test_clin" value="test/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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404 <param name="train_omics_main" value="train/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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405 <param name="test_omics_main" value="test/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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406 <param name="assay_main" value="bar"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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407 <param name="layer_main" value="input"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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408 <repeat name="omics">

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409 <param name="train_omics" value="train/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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410 <param name="test_omics" value="test/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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411 <param name="assay" value="foo"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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412 <param name="layer" value="output"/>

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413 </repeat>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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414 <conditional name="training_type">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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415 <param name="model" value="cm_train"/>

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416 <param name="model_class" value="CrossModalPred"/>

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417 </conditional>

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418 <param name="hpo_iter" value="1"/>

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419 <output_collection name="results" type="list">

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420 <element name="job.embeddings_test">

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421 <assert_contents>

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422 <has_n_lines n="50"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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423 </assert_contents>

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424 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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425 <element name="job.embeddings_train">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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426 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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427 <has_n_lines n="50"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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428 </assert_contents>

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429 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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430 <element name="job.feature_logs.bar">

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431 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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432 <has_n_lines n="25"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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433 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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434 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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435 <element name="job.feature_logs.omics_foo">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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436 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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437 <has_n_lines n="25"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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438 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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439 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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440 <element name="job.test_decoded.omics_foo">

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441 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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442 <has_n_lines n="23"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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443 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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444 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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445 <element name="job.train_decoded.omics_foo">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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446 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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447 <has_n_lines n="23"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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448 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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449 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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450 </output_collection>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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451 </test>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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452 <test>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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453 <param name="non_commercial_use" value="True"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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diff changeset

454 <param name="train_clin" value="train/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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455 <param name="test_clin" value="test/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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456 <param name="train_omics_main" value="train/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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457 <param name="test_omics_main" value="test/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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458 <param name="assay_main" value="bar"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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459 <repeat name="omics">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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460 <param name="train_omics" value="train/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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461 <param name="test_omics" value="test/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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462 <param name="assay" value="foo"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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463 </repeat>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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diff changeset

464 <conditional name="training_type">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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465 <param name="model" value="s_train"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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466 <param name="model_class" value="GNN"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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467 <param name="gnn_conv_type" value="GC"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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468 <param name="string_organism" value="9606"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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469 <param name="string_node_name" value="gene_name"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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470 <param name="target_variables" value="Erlotinib"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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471 </conditional>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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472 <param name="hpo_iter" value="1"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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473 <output_collection name="results" type="list">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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474 <element name="job.embeddings_test">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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475 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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476 <has_n_lines n="50"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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477 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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478 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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479 <element name="job.embeddings_train">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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480 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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481 <has_n_lines n="50"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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482 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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483 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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484 <element name="job.feature_importance">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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485 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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486 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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487 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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488 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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489 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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490 <element name="job.feature_logs.bar">

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491 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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492 <has_n_lines n="25"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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493 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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494 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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495 <element name="job.feature_logs.omics_foo">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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496 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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497 <has_n_lines n="25"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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498 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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499 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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500 <element name="job.predicted_labels">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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501 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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502 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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503 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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504 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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505 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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506 <element name="job.stats">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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507 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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508 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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509 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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510 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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511 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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512 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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513 </output_collection>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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514 </test>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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515 <test>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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516 <param name="non_commercial_use" value="True"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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517 <param name="train_clin" value="train/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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518 <param name="test_clin" value="test/clin" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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519 <param name="train_omics_main" value="train/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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520 <param name="test_omics_main" value="test/gex" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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521 <param name="assay_main" value="b ar"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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522 <repeat name="omics">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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523 <param name="train_omics" value="train/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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524 <param name="test_omics" value="test/cnv" ftype="csv"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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525 <param name="assay" value="f oo"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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526 </repeat>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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527 <conditional name="training_type">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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528 <param name="model" value="us_train"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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529 <param name="model_class" value="supervised_vae"/>

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530 </conditional>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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531 <param name="hpo_iter" value="1"/>

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532 <output_collection name="results" type="list">

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533 <element name="job.embeddings_test">

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534 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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535 <has_n_lines n="50"/>

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536 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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537 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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538 <element name="job.embeddings_train">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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539 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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540 <has_n_lines n="50"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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541 </assert_contents>

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542 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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543 <element name="job.feature_logs.b_ar">

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544 <assert_contents>

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545 <has_n_lines n="25"/>

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546 </assert_contents>

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547 </element>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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548 <element name="job.feature_logs.omics_f_oo">

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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549 <assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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550 <has_n_lines n="25"/>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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551 </assert_contents>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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552 </element>

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553 </output_collection>

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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554 </test>

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555 </tests>

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556 <help>

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557 .. class:: warningmark

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558

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559 **WARNING: This tool is only available for NON-COMMERCIAL use. Permission is only granted for academic, research, and educational purposes. Before using, be sure to review, agree, and comply with the license.**

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560

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561 Flexynesis is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.

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562 The package includes multiple types of deep learning architectures such as simple fully connected networks, supervised variational autoencoders, graph convolutional networks, multi-triplet networks different options of data layer fusion, and automates feature selection and hyperparameter optimisation.

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563

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564 For more information, please check the Documentation_ :

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565

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566 For commercial use, please review the license_ and contact the `copyright holders`_ .

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567

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568 -----

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569

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570 .. image:: https://raw.githubusercontent.com/BIMSBbioinfo/flexynesis/c4634d97f84e51f569dcfdab2caf42c9be453ef6/img/graphical_abstract.jpg

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571 :width: 600

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572

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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573 -----

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574

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575 **Input Files**

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576

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577 **clin.csv**

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578

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579 clin.csv contains the sample metadata. The first column contains unique sample identifiers. The other columns contain sample-associated clinical variables. NA values are allowed in the clinical variables.

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580

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581 The format might look like so:

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582

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583 ======== === === ===

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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584 , v1 v2 ...

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585 -------- --- --- ---

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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586 sample1 a b ...

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587 -------- --- --- ---

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588 sample2 c d ...

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589 -------- --- --- ---

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590 sample3 e f ...

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591 -------- --- --- ---

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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592 ... ... ... ...

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593 ======== === === ===

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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594

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595 .

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596

98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb

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597 **omics.csv**

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598

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599 The first column of the feature tables must be unique feature identifiers (e.g. gene names). The column names must be sample identifiers that should overlap with those in the clin.csv. They don't have to be completely identical or in the same order. Samples from the clin.csv that are not represented in the omics table will be dropped.

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600

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601 The format might look like so:

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602

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603 ===== ======= ======= ======= =======

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604 , sample1 sample2 sample3 ...

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605 ----- ------- ------- ------- -------

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606 gene1 0 1 2 ...

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607 ----- ------- ------- ------- -------

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608 gene2 3 3 5 ...

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609 ----- ------- ------- ------- -------

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610 gene3 2 3 4 ...

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611 ----- ------- ------- ------- -------

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612 ... ... ... ... ...

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613 ===== ======= ======= ======= =======

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614

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615 .

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616

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617 .. class:: infomark

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618

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619 **Concordance between train/test splits:**

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620

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621 The corresponding omics files in train/test splits must contain overlapping feature names (they don't have to be identical or in the same order). The clin.csv files in train/test must contain matching clinical variables.

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622

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623 -----

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624

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625 **Supervised Training**

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626

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627 **Minimum requirements**

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628

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629 * clin.csv and omics.csv files for training and testing

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630 * Selection of a tool/model

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631 * One target variable which can be numerical or categorical for regression/classification tasks.

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632

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633 Flexynesis supports both single-task and multi-task training. We can provide one or more target variables and optionally survival variables as input and Flexynesis will build the appropriate model architecture. If the selected variable is numerical, a Multi-Layered-Perceptron (MLP) with MSE loss will be used. If a categorical variable is provided, an MLP with cross-entropy-loss will be utilized. If survival variables are provided, an MLP with Cox-Proportional-Hazards loss will be attached to the model.

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634

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635 **Regression:**

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636

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637

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638 If your target variable is numerical, Flexynesis will build a regression model.

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639

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640 **Classification:**

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641

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642

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643 If your target variable is categorical, Flexynesis will build a classification model.

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644

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645 **Survival Analysis:**

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646

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647

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648 If your target variable is survival data, Flexynesis will build a survival analysis model.

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649 For survival analysis, two separate variables are required, where the first variable is a numeric event variable (consisting of 0's or 1's, where 1 means an event such as disease progression or death has occurred). The second variable is also a numeric time variable, which indicates how much time it took since last patient follow-up.

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650

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651 .. class:: infomark

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652

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653 **Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks.

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654

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655 .. class:: infomark

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656

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657 **Note:** For the supervised tasks, the user can easily switch between different model architectures.

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658

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659 .. class:: infomark

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660

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661 **Note:** If you choose **MultiTripletNetwork** model, the first target variable should be a categorical variable.

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662

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663 .. class:: infomark

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664

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665 **Note:** If you choose **GNN** model, the features should have the same naming convention between different omics modalities.

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666

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667 .. class:: infomark

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668

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669 **Note:** The **GNN** model only works with genes (for example CpG methylation sites does not work). The reason is that GNNs require a prior knowledge network, which is currently set to use STRING database.

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670

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671 -----

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672

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673 **Unsupervised Training**

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674

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675 In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training.

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676

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677 -----

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678

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679 **Cross-modality Training**

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680

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681 We have implemented a special case of VAEs where the input data layers and output data layers can be set to different data modalities. The purpose of a cross-modality encoder is to learn embeddings that can translate from one data modality to another. Crossmodality encoder we implemented supports both single/multiple input layers and also one or more target/survival variables can be added to the model.

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682

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683 .. class:: infomark

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684

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685 **Note:** if you use same input and output layers, it will be the same as unsupervised training.

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686

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687 -----

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688

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689 .. class:: infomark

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690

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691 **Modality fusion:**

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692

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693 Flexynesis currently supports two main ways of fusing different omics data modalities: 1. Early fusion: The input data matrices are initially concatenated and pushed through the networks 2. Intermediate fusion: The input data matrices are initially pushed through the networks to obtain a modality-specific embedding space, which then gets concatenated to serve as input for the supervisor MLPs.

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694

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695 .. _license: https://github.com/BIMSBbioinfo/flexynesis/blob/main/LICENSE

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696 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/

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697 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis

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698 </help>

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699

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700 <expand macro="citations" />

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701 </tool>

Mercurial > repos > bgruening > flexynesis

annotate flexynesis.xml @ 0:98431bd19f18 draft