flexynesis_plot: flexynesis

annotate flexynesis_plot.xml @ 4:07f018886d40 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a

author	bgruening
date	Fri, 04 Jul 2025 14:58:49 +0000
parents	1b0e4bd4815b
children	07f595f34f29

rev	line source
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	1 <tool id="flexynesis_plot" name="Flexynesis plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	2 <description>tool for visualizing flexynesis results</description>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	3 <macros>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	4 <import>macros.xml</import>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	5 </macros>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	6 <expand macro="requirements"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	7 <required_files>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	8 <include path="flexynesis_plot.py" />
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	9 </required_files>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	11 @CHECK_NON_COMMERCIAL_USE@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	12 mkdir -p inputs/ plots/ &&
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	13 ln -s '$plot_conditional.labels' 'inputs/$plot_conditional.labels.element_identifier.$plot_conditional.labels.ext' &&
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	14 #if $plot_conditional.plot_type == "dimred":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	15 ln -s '$plot_conditional.embeddings' 'inputs/$plot_conditional.embeddings.element_identifier.$plot_conditional.embeddings.ext' &&
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	16 #end if
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	17 cat '$flexynesis_plot_config' &&
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	18 python '$flexynesis_plot_config'
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	19 ]]></command>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	20 <configfiles>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	21 <configfile name="flexynesis_plot_config"><![CDATA[
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	22 import sys
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	23 sys.path.append('$__tool_directory__/')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	24
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	25 import matplotlib.pyplot as plt
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	26 import numpy as np
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	27 import pandas as pd
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	28 import seaborn as sns
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	29 import torch
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	30 from flexynesis import (
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	31 get_important_features,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	32 plot_dim_reduced,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	33 plot_hazard_ratios,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	34 plot_kaplan_meier_curves,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	35 plot_pr_curves,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	36 plot_roc_curves,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	37 plot_scatter
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	38 )
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	39 from scipy.stats import kruskal, mannwhitneyu
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	40 from flexynesis_plot import (
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	41 plot_label_concordance_heatmap,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	42 plot_boxplot,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	43 detect_color_type,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	44 load_labels,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	45 load_embeddings,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	46 match_samples_to_embeddings
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	47 )
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	48 #if $plot_conditional.plot_type == "dimred":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	49 @PLOT_COMMON_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	50 embeddings, sample_names = load_embeddings('inputs/$plot_conditional.embeddings.element_identifier.$plot_conditional.embeddings.ext')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	51 matched_labels = match_samples_to_embeddings(sample_names, label_data)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	52
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	53 label = matched_labels.columns[$plot_conditional.label-1]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	54 color_type = detect_color_type(matched_labels[label])
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	55
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	56 fig = plot_dim_reduced(
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	57 matrix=embeddings,
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	58 labels=matched_labels[label],
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	59 method='$plot_conditional.method',
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	60 color_type=color_type
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	61 )
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	62 output_path = "plots/{label}_${plot_conditional.method}.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	63 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	64 #else if $plot_conditional.plot_type == "scatter":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	65 @PLOT_COMMON_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	66
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	67 true_label = label_data.columns[$plot_conditional.true_label-1]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	68 predicted_label = label_data.columns[$plot_conditional.predicted_label-1]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	69 true_values = pd.to_numeric(label_data[true_label], errors='coerce')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	70 predicted_values = pd.to_numeric(label_data[predicted_label], errors='coerce')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	71
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	72 if true_values.isna().all() or predicted_values.isna().all():
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	73 raise ValueError("No valid numeric values found for known or predicted labels")
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	74
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	75 fig = plot_scatter(true_values, predicted_values)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	76
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	77 output_path = "plots/${plot_conditional.true_label}_${plot_conditional.predicted_label}_scatter.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	78 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	79
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	80 #else if $plot_conditional.plot_type == "concordance_heatmap":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	81 @PLOT_COMMON_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	82
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	83 true_label = label_data.columns[$plot_conditional.true_label-1]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	84 predicted_label = label_data.columns[$plot_conditional.predicted_label-1]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	85
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	86 true_values = label_data[true_label].tolist()
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	87 predicted_values = label_data[predicted_label].tolist()
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	88 fig = plot_label_concordance_heatmap(true_values, predicted_values)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	89 plt.close(fig)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	90 output_path = "plots/{true_label}_{predicted_label}_concordance_heatmap.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	91 fig.savefig(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	92
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	93 #else if $plot_conditional.plot_type == "pr_curve":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	94 @PR_ROC_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	95
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	96 fig = plot_pr_curves(y_true_np, y_probs_np)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	97
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	98 output_path = "plots/pr_curves.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	99 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	100
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	101 #else if $plot_conditional.plot_type == "roc_curve":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	102 @PR_ROC_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	103 fig = plot_roc_curves(y_true_np, y_probs_np)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	104 output_path = "plots/roc_curves.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	105 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	106
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	107 #else if $plot_conditional.plot_type == "box_plot":
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	108 @PR_ROC_BOX_CONFIG@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	109 # Remove rows with missing data
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	110 clean_data = label_data.dropna(subset=['known_label', 'probability'])
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	111
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	112 if clean_data.empty:
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	113 raise ValueError(" No valid data after cleaning")
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	114
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	115 # Get unique classes
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	116 classes = clean_data['class_label'].unique()
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	117
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	118 for class_label in classes:
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	119 print(f" Generating box plot for class: {class_label}")
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	120
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	121 # Filter for current class
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	122 class_data = clean_data[clean_data['class_label'] == class_label]
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	123
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	124 # Create the box plot
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	125 fig = plot_boxplot(
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	126 categorical_x=class_data['known_label'],
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	127 numerical_y=class_data['probability'],
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	128 title_x='True Label',
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	129 title_y=f'Predicted Probability ({class_label})',
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	130 )
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	131
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	132 # Save the plot
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	133 safe_class_name = str(class_label).replace('/', '_').replace('\\', '_').replace(' ', '_').replace(':', '_')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	134 plt.close(fig)
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	135
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	136 output_path = f"plots/box_plot_{safe_class_name}.${plot_conditional.format}"
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	137 fig.savefig(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	138 #end if
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	139 ]]></configfile>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	140 </configfiles>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	141 <inputs>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	142 <expand macro="commercial_use_param"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	143 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	144 <param name="plot_type" type="select" label="Flexynesis plot">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	145 <option value="dimred">Dimensionality reduction</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	146 <option value="scatter">Scatter plot of known vs predicted labels</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	147 <option value="concordance_heatmap">Label concordance heatmap</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	148 <option value="pr_curve">Precision-recall curves</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	149 <option value="roc_curve">ROC curves</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	150 <option value="box_plot">Box plot</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	151 </param>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	152 <when value="dimred">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	153 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	154 <expand macro="plots_common_input"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	155 <param argument="--embeddings" type="data" format="tabular" label="Embeddings" help="Generated by flexynesis"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	156 <param argument="--label" type="data_column" data_ref="labels" label="Column in the labels file to use for coloring the points in the plot"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	157 <param name="method" type="select" label="Transformation method">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	158 <option value="pca" selected="true">PCA</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	159 <option value="umap">UMAP</option>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	160 </param>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	161 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	162 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	163 <when value="scatter">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	164 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	165 <expand macro="plots_common_input"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	166 <param name="true_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the true labels"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	167 <param name="predicted_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the predicted labels"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	168 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	169 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	170 <when value="concordance_heatmap">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	171 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	172 <expand macro="plots_common_input"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	173 <param name="true_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the true labels"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	174 <param name="predicted_label" type="data_column" data_ref="labels" label="Column name in the labels file to use for the predicted labels"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	175 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	176 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	177 <when value="pr_curve">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	178 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	179 <expand macro="plots_common_input"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	180 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	181 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	182 <when value="roc_curve">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	183 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	184 <expand macro="plots_common_input"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	185 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	186 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	187 <when value="box_plot">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	188 <expand macro="plots_common_param">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	189 <expand macro="plots_common_input"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	190 </expand>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	191 </when>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	192 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	193 </inputs>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	194 <outputs>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	195 <data name="plot_out" auto_format="true" from_work_dir="plots/*" label="${tool.name} on ${on_string}: ${plot_conditional.plot_type}">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	196 <filter>plot_conditional['plot_type'] != "box_plot"</filter>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	197 </data>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	198 <collection name="boxplot_out" type="list" label="${tool.name} on ${on_string}: box_plot">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	199 <discover_datasets pattern="__name_and_ext__" directory="plots/"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	200 <filter>plot_conditional['plot_type'] == "box_plot"</filter>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	201 </collection>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	202 </outputs>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	203 <tests>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	204 <!-- test 1: dimred -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	205 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	206 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	207 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	208 <param name="plot_type" value="dimred"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	209 <param name="embeddings" value="embeddings.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	210 <param name="label" value="6"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	211 <param name="method" value="pca"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	212 <param name="labels" value="labels.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	213 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	214 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	215 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	216 <output name="plot_out">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	217 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	218 <has_image_center_of_mass center_of_mass="970,733" eps="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	219 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	220 <has_image_height height="1461" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	221 <has_image_width width="1941" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	222 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	223 </output>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	224 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	225 <!-- test 2: scatter -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	226 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	227 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	228 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	229 <param name="plot_type" value="scatter"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	230 <param name="labels" value="labels_scatter.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	231 <param name="true_label" value="5"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	232 <param name="predicted_label" value="6"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	233 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	234 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	235 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	236 <output name="plot_out">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	237 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	238 <has_image_center_of_mass center_of_mass="970,733" eps="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	239 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	240 <has_image_height height="1461" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	241 <has_image_width width="1941" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	242 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	243 </output>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	244 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	245 <!-- test 3: concordance_heatmap -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	246 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	247 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	248 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	249 <param name="plot_type" value="concordance_heatmap"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	250 <param name="labels" value="labels.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	251 <param name="true_label" value="5"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	252 <param name="predicted_label" value="6"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	253 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	254 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	255 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	256 <output name="plot_out">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	257 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	258 <has_image_center_of_mass center_of_mass="1450,1310" eps="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	259 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	260 <has_image_height height="2558" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	261 <has_image_width width="2770" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	262 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	263 </output>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	264 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	265 <!-- test 4: pr_curve -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	266 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	267 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	268 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	269 <param name="plot_type" value="pr_curve"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	270 <param name="labels" value="labels_pr.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	271 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	272 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	273 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	274 <output name="plot_out">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	275 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	276 <has_image_center_of_mass center_of_mass="970,733" eps="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	277 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	278 <has_image_height height="1461" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	279 <has_image_width width="1941" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	280 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	281 </output>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	282 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	283 <!-- test 5: roc_curve -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	284 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	285 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	286 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	287 <param name="plot_type" value="roc_curve"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	288 <param name="labels" value="labels_pr.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	289 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	290 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	291 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	292 <output name="plot_out">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	293 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	294 <has_image_center_of_mass center_of_mass="970,733" eps="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	295 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	296 <has_image_height height="1461" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	297 <has_image_width width="1941" delta="50"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	298 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	299 </output>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	300 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	301 <!-- test 6: box_plot -->
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	302 <test expect_num_outputs="1">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	303 <param name="non_commercial_use" value="True"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	304 <conditional name="plot_conditional">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	305 <param name="plot_type" value="box_plot"/>
4 07f018886d40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a bgruening parents: 0 diff changeset	306 <param name="labels" value="labels_pr.tabular"/>
0 1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	307 <param name="format" value="jpg"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	308 <param name="dpi" value="300"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	309 </conditional>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	310 <output_collection name="boxplot_out" type="list" count="7">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	311 <element name="box_plot_Basal">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	312 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	313 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	314 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	315 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	316 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	317 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	318 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	319 <element name="box_plot_Her2">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	320 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	321 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	322 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	323 <has_image_height height="1765" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	324 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	325 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	326 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	327 <element name="box_plot_LumA">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	328 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	329 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	330 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	331 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	332 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	333 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	334 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	335 <element name="box_plot_LumB">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	336 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	337 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	338 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	339 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	340 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	341 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	342 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	343 <element name="box_plot_NC">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	344 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	345 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	346 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	347 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	348 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	349 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	350 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	351 <element name="box_plot_Normal">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	352 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	353 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	354 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	355 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	356 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	357 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	358 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	359 <element name="box_plot_claudin-low">
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	360 <assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	361 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	362 <has_image_channels channels="3"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	363 <has_image_height height="1783" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	364 <has_image_width width="2967" delta="20"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	365 </assert_contents>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	366 </element>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	367 </output_collection>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	368 </test>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	369 </tests>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	370 <help><![CDATA[
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	371 @COMMON_HELP@
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	372
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	373 Flexynesis plot is a comprehensive visualization tool designed to create various types of plots for analyzing machine learning results from the Flexynesis framework. This tool supports multiple visualization types to help researchers understand their data and model performance.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	374
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	375 Available plot types include:
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	376
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	377 - Dimensionality Reduction: Visualizes high-dimensional data in a lower-dimensional space using methods like PCA or UMAP.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	378 - Scatter Plot: Compares known and predicted labels to assess model performance.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	379 - Label Concordance Heatmap: Displays the agreement between true and predicted labels in a heatmap format.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	380 - Precision-Recall Curves: Plots precision against recall to evaluate the trade-off between these metrics.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	381 - ROC Curves: Visualizes the true positive rate against the false positive rate to assess model discrimination.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	382 - Box Plot: Shows the distribution of predicted probabilities across different classes, highlighting medians and quartiles.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	383
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	384
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	385 Input Files
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	386
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	387 Main common input file is the labels file, which is the predicted labels file generated by Flexynesis. It should contain the following columns:
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	388
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	389 - `sample_id`: Unique identifier for each sample.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	390 - `variable`: The target variable used for the analysis.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	391 - `class_label`: The class labels for the samples, used in box plots.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	392 - `probability`: The predicted probabilities for the labels.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	393 - `known_label`: The true labels for the samples, used in scatter plots and concordance heatmaps.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	394 - `predicted_label`: The labels predicted by the Flexynesis model, used in scatter plots and concordance heatmaps.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	395
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	396
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	397 For dimensionality reduction plots, an additional embeddings file is required, which contains the reduced-dimensional representations of the samples. This file is generated by Flexynesis.
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	398
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	399
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	400 .. class:: warningmark
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	401
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	402 PR and ROC curves can only be applied on classification tasks!
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	403
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	404
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	405 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	406 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	407 ]]></help>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	408 <expand macro="creator"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	409 <expand macro="citations"/>
1b0e4bd4815b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	410 </tool>

Mercurial > repos > bgruening > flexynesis_plot

annotate flexynesis_plot.xml @ 4:07f018886d40 draft