flexynesis: flexynesis.xml annotate

annotate flexynesis.xml @ 1:b353dad17ab7 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4

author	bgruening
date	Mon, 14 Apr 2025 09:56:16 +0000
parents	98431bd19f18
children

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
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	74 --val_size $val_size
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	75 --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	76 --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	77 --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	78 --subsample $subsample
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	79 --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	80 --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	81 --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	82 --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	83 --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	84 $log_transform
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	85 $use_loss_weighting
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	86 $use_cv
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	87 $evaluate_baseline_performance
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	88 --feature_importance_method $feature_importance_method
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	89 $disable_marker_finding
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	90 \${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	91 ]]></command>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	92 <inputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	93 <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	94 <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	95 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	96 <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	97 <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	98 <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	99 <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	100 <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	101 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	102 <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	103 <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	104 <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	105 <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	106 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	107 <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	108 <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	109 <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	110 <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	111 <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	112 <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	113 <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	114 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	115 <option value="XGBoost">XGBoost</option>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	116 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	117 <when value="DirectPred"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	118 <when value="GNN">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	119 <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	120 <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	121 <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	122 <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	123 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	124 <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	125 <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	126 <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	127 <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	128 <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	129 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	130 <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	131 <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	132 <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	133 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	134 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	135 <when value="MultiTripletNetwork"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	136 <when value="RandomForest"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	137 <when value="SVM"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	138 <when value="RandomSurvivalForest"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	139 <when value="XGBoost"/>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	140 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	141 <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	142 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	143 <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	144 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	145 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	146 <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	147 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	148 <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	149 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	150 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	151 <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	152 <sanitizer invalid_char="">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	153 <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	154 </sanitizer>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	155 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	156 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	157 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	158 <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	159 <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	160 <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	161 <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	162 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	163 <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	164 <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	165 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	166 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	167 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	168 <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	169 <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	170 <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	171 <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	172 <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	173 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	174 <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	175 <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	176 <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	177 <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	178 <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	179 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	180 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	181 <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	182 <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	183 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	184 <expand macro="advanced"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	185 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	186 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	187 </inputs>
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 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	190 <discover_datasets pattern="(?P<name>.+)\.csv$" 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	191 </collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	192 </outputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	193 <tests>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	194 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	195 <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	196 <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	197 <param name="model" value="s_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	198 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	199 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	200 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	201 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	202 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	203 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	204 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	205 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	206 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	207 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	208 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	209 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	210 </conditional>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	211 <param name="target_variables" value="Erlotinib"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	212 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	213 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	214 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	215 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	216 <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	217 <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	218 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	219 <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	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 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	222 <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	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 <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	225 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	226 </element>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	227 <element name="job.feature_importance.GradientShap">
0 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 <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	230 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	231 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	232 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	233 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	234 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	235 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	236 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	237 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	238 <has_text_matching expression="IntegratedGradients"/>
0 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.feature_logs.bar">
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_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	244 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	245 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	246 <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	247 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	248 <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	249 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	250 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	251 <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	252 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	253 <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	254 <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	255 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	256 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	257 <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	258 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	259 <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	260 <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	261 <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	262 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	263 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	264 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	265 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	266 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	267 <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	268 <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	269 <param name="model" value="s_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	270 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	271 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	272 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	273 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	274 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	275 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	276 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	277 </conditional>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	278 <param name="target_variables" value="Erlotinib"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	279 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	280 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	281 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	282 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	283 <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	284 <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	285 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	286 <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	287 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	288 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	289 <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	290 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	291 <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	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 </element>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	294 <element name="job.feature_importance.GradientShap">
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	295 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	296 <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	297 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	298 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	299 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	300 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	301 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	302 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	303 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	304 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	305 <has_text_matching expression="IntegratedGradients"/>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	306 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	307 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	308 <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	309 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	310 <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	311 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	312 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	313 <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	314 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	315 <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	316 <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	317 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	318 </element>
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.stats">
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_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	322 <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	323 <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	324 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	325 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	326 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	327 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	328 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	329 <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	330 <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	331 <param name="model" value="s_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	332 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	333 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	334 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	335 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	336 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	337 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	338 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	339 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	340 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	341 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	342 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	343 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	344 </conditional>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	345 <param name="target_variables" value="Irinotecan"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	346 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	347 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	348 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	349 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	350 <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	351 <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	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_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	354 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	355 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	356 <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	357 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	358 <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	359 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	360 </element>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	361 <element name="job.feature_importance.GradientShap">
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	362 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	363 <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	364 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	365 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	366 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	367 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	368 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	369 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	370 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	371 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	372 <has_text_matching expression="IntegratedGradients"/>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	373 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	374 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	375 <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	376 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	377 <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	378 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	379 </element>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	380 <element name="job.feature_logs.omics_foo">
0 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 <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	383 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	384 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	385 <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	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 <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	388 <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	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 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	391 <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	392 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	393 <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	394 <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	395 <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	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 <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	403 <param name="model" value="us_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	404 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	405 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	406 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	407 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	408 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	409 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	410 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	411 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	412 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	413 </repeat>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	414 <param name="model_class" value="supervised_vae"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	415 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	416 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	417 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	418 </conditional>
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 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	441 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	442 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	443 <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	444 <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	445 <param name="model" value="cm_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	446 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	447 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	448 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	449 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	450 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	451 <param name="layer_main" value="input"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	452 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	453 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	454 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	455 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	456 <param name="layer" value="output"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	457 </repeat>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	458 <param name="model_class" value="CrossModalPred"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	459 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	460 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	461 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	462 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	463 <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	464 <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	465 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	466 <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	467 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	468 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	469 <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	470 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	471 <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	472 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	473 </element>
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.feature_logs.bar">
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="25"/>
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.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	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="25"/>
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.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	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_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	487 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	488 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	489 <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	490 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	491 <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	492 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	493 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	494 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	495 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	496 <test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	497 <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	498 <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	499 <param name="model" value="s_train"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	500 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	501 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	502 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	503 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	504 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	505 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	506 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	507 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	508 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	509 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	510 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	511 <param name="model_class" value="GNN"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	512 <param name="gnn_conv_type" value="GC"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	513 <param name="string_organism" value="9606"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	514 <param name="string_node_name" value="gene_name"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	515 </conditional>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	516 <param name="target_variables" value="Erlotinib"/>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	517 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	518 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	519 </section>
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	520 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	521 <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	522 <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	523 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	524 <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	525 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	526 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	527 <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	528 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	529 <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	530 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	531 </element>
1 b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	532 <element name="job.feature_importance.GradientShap">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	533 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	534 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	535 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	536 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	537 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	538 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	539 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	540 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	541 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	542 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	543 <has_text_matching expression="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	544 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	545 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	546 <element name="job.feature_logs.bar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	547 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	548 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	549 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	550 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	551 <element name="job.feature_logs.omics_foo">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	552 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	553 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	554 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	555 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	556 <element name="job.predicted_labels">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	557 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	558 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	559 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	560 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	561 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	562 <element name="job.stats">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	563 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	564 <has_text_matching expression="GNN,Erlotinib,numerical,mse,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	565 <has_text_matching expression="GNN,Erlotinib,numerical,r2,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	566 <has_text_matching expression="GNN,Erlotinib,numerical,pearson_corr,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	567 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	568 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	569 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	570 </test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	571 <test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	572 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	573 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	574 <param name="model" value="us_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	575 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	576 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	577 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	578 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	579 <param name="assay_main" value="b ar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	580 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	581 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	582 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	583 <param name="assay" value="f oo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	584 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	585 <param name="model_class" value="supervised_vae"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	586 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	587 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	588 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	589 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	590 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	591 <element name="job.embeddings_test">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	592 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	593 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	594 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	595 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	596 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	597 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	598 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	599 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	600 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	601 <element name="job.feature_logs.b_ar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	602 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	603 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	604 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	605 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	606 <element name="job.feature_logs.omics_f_oo">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	607 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	608 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	609 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	610 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	611 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	612 </test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	613 <test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	614 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	615 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	616 <param name="model" value="s_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	617 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	618 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	619 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	620 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	621 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	622 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	623 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	624 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	625 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	626 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	627 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	628 <param name="model_class" value="XGBoost"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	629 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	630 <param name="target_variables" value="Erlotinib"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	631 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	632 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	633 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	634 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	635 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	636 <element name="job.stats">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	637 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	638 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,mse,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	639 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,r2,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	640 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,pearson_corr,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	641 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	642 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	643 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	644 </test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	645 <test>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	646 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	647 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	648 <param name="model" value="s_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	649 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	650 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	651 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	652 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	653 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	654 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	655 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	656 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	657 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	658 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	659 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	660 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	661 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	662 <param name="target_variables" value="Erlotinib"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	663 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	664 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	665 <param name="feature_importance_method" value="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	666 <param name="val_size" value="0.2"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	667 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	668 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	669 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	670 <element name="job.embeddings_test">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	671 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	672 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	673 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	674 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	675 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	676 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	677 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	678 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	679 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4 bgruening parents: 0 diff changeset	680 <element name="job.feature_importance.IntegratedGradients">
0 98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	681 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	682 <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	683 <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	684 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	685 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	686 <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	687 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	688 <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	689 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	690 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	691 <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	692 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	693 <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	694 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	695 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	696 <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	697 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	698 <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	699 <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	700 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	701 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	702 <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	703 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	704 <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	705 <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	706 <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	707 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	708 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	709 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	710 </test>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	711 </tests>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	712 <help>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	713 .. class:: warningmark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	714
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	715 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	716
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	717 Flexynesis is a deep-learning based multi-omics bulk sequencing data integration suite with a focus on (pre-)clinical endpoint prediction.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	718 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	719
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	720 For more information, please check the Documentation_ :
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	721
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	722 For commercial use, please review the license_ and contact the `copyright holders`_ .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	723
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	724 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	725
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	726 .. image:: https://raw.githubusercontent.com/BIMSBbioinfo/flexynesis/c4634d97f84e51f569dcfdab2caf42c9be453ef6/img/graphical_abstract.jpg
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	727 :width: 600
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	728
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	729 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	730
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	731 Input Files
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	732
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	733 clin.csv
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	734
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	735 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	736
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	737 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	738
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	739 ======== === === ===
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	740 , v1 v2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	741 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	742 sample1 a b ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	743 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	744 sample2 c d ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	745 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	746 sample3 e f ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	747 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	748 ... ... ... ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	749 ======== === === ===
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	750
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	751 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	752
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	753 omics.csv
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	754
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	755 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	756
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	757 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	758
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	759 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	760 , sample1 sample2 sample3 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	761 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	762 gene1 0 1 2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	763 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	764 gene2 3 3 5 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	765 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	766 gene3 2 3 4 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	767 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	768 ... ... ... ... ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	769 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	770
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	771 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	772
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	773 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	774
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	775 Concordance between train/test splits:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	776
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	777 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	778
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	779 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	780
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	781 Supervised Training
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	782
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	783 Minimum requirements
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	784
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	785 * clin.csv and omics.csv files for training and testing
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	786 * Selection of a tool/model
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	787 * One target variable which can be numerical or categorical for regression/classification tasks.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	788
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	789 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	790
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	791 Regression:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	792
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	793
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	794 If your target variable is numerical, Flexynesis will build a regression model.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	795
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	796 Classification:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	797
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	798
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	799 If your target variable is categorical, Flexynesis will build a classification model.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	800
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	801 Survival Analysis:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	802
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	803
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	804 If your target variable is survival data, Flexynesis will build a survival analysis model.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	805 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	806
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	807 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	808
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	809 Note: Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	810
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	811 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	812
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	813 Note: For the supervised tasks, the user can easily switch between different model architectures.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	814
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	815 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	816
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	817 Note: If you choose MultiTripletNetwork model, the first target variable should be a categorical variable.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	818
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	819 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	820
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	821 Note: If you choose GNN model, the features should have the same naming convention between different omics modalities.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	822
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	823 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	824
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	825 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	826
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	827 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	828
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	829 Unsupervised Training
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	830
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	831 In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	832
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	833 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	834
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	835 Cross-modality Training
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	836
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	837 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	838
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	839 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	840
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	841 Note: if you use same input and output layers, it will be the same as unsupervised training.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	842
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	843 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	844
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	845 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	846
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	847 Modality fusion:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	848
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	849 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.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	850
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	851 .. _license: https://github.com/BIMSBbioinfo/flexynesis/blob/main/LICENSE
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	852 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	853 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	854 </help>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	855
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	856 <expand macro="citations" />
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb bgruening parents: diff changeset	857 </tool>

Mercurial > repos > bgruening > flexynesis

annotate flexynesis.xml @ 1:b353dad17ab7 draft default tip