flexynesis_plot: flexynesis

annotate flexynesis_plot.xml @ 2:3c5d82bf6e8a draft

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

author	bgruening
date	Fri, 04 Jul 2025 14:57:52 +0000
parents	bb91bf19eb40
children	52b6f2ac38c7

rev	line source
0 bb91bf19eb40 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@">
bb91bf19eb40 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>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	3 <macros>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	4 <import>macros.xml</import>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	5 </macros>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	6 <expand macro="requirements"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	7 <required_files>
bb91bf19eb40 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" />
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	9 </required_files>
bb91bf19eb40 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[
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	11 @CHECK_NON_COMMERCIAL_USE@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	12 mkdir -p inputs/ plots/ &&
bb91bf19eb40 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' &&
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	14 #if $plot_conditional.plot_type == "dimred":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	15 ln -s '$plot_conditional.embeddings' 'inputs/$plot_conditional.embeddings.element_identifier.$plot_conditional.embeddings.ext' &&
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	16 #end if
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	17 cat '$flexynesis_plot_config' &&
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	18 python '$flexynesis_plot_config'
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	19 ]]></command>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	20 <configfiles>
bb91bf19eb40 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[
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	22 import sys
bb91bf19eb40 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__/')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	24
bb91bf19eb40 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
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	26 import numpy as np
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	27 import pandas as pd
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	28 import seaborn as sns
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	29 import torch
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	30 from flexynesis import (
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	31 get_important_features,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	32 plot_dim_reduced,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	33 plot_hazard_ratios,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	34 plot_kaplan_meier_curves,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	35 plot_pr_curves,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	36 plot_roc_curves,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	37 plot_scatter
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	38 )
bb91bf19eb40 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
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	40 from flexynesis_plot import (
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	41 plot_label_concordance_heatmap,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	42 plot_boxplot,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	43 detect_color_type,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	44 load_labels,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	45 load_embeddings,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	46 match_samples_to_embeddings
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	47 )
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	48 #if $plot_conditional.plot_type == "dimred":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	49 @PLOT_COMMON_CONFIG@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	50 embeddings, sample_names = load_embeddings('inputs/$plot_conditional.embeddings.element_identifier.$plot_conditional.embeddings.ext')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	51 matched_labels = match_samples_to_embeddings(sample_names, label_data)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	52
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	53 label = matched_labels.columns[$plot_conditional.label-1]
bb91bf19eb40 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])
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	55
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	56 fig = plot_dim_reduced(
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	57 matrix=embeddings,
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	58 labels=matched_labels[label],
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	59 method='$plot_conditional.method',
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	60 color_type=color_type
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	61 )
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	62 output_path = "plots/{label}_${plot_conditional.method}.${plot_conditional.format}"
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	63 fig.save(output_path, dpi=$plot_conditional.dpi, bbox_inches='tight')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	64 #else if $plot_conditional.plot_type == "scatter":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	65 @PLOT_COMMON_CONFIG@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	66
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	67 true_label = label_data.columns[$plot_conditional.true_label-1]
bb91bf19eb40 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]
bb91bf19eb40 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')
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	71
bb91bf19eb40 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():
bb91bf19eb40 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")
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	74
bb91bf19eb40 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)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	76
bb91bf19eb40 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}"
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	79
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	80 #else if $plot_conditional.plot_type == "concordance_heatmap":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	81 @PLOT_COMMON_CONFIG@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	82
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	83 true_label = label_data.columns[$plot_conditional.true_label-1]
bb91bf19eb40 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[$plot_conditional.predicted_label-1]
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	85
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	86 true_values = label_data[true_label].tolist()
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	87 predicted_values = label_data[predicted_label].tolist()
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	88 fig = plot_label_concordance_heatmap(true_values, predicted_values)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	89 plt.close(fig)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	90 output_path = "plots/{true_label}_{predicted_label}_concordance_heatmap.${plot_conditional.format}"
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	92
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	93 #else if $plot_conditional.plot_type == "pr_curve":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	94 @PR_ROC_CONFIG@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	95
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	96 fig = plot_pr_curves(y_true_np, y_probs_np)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	97
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	98 output_path = "plots/pr_curves.${plot_conditional.format}"
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	100
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	101 #else if $plot_conditional.plot_type == "roc_curve":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	102 @PR_ROC_CONFIG@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	103 fig = plot_roc_curves(y_true_np, y_probs_np)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	104 output_path = "plots/roc_curves.${plot_conditional.format}"
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	106
bb91bf19eb40 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":
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	108 @PR_ROC_BOX_CONFIG@
bb91bf19eb40 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
bb91bf19eb40 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'])
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	111
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	112 if clean_data.empty:
bb91bf19eb40 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")
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	114
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	115 # Get unique classes
bb91bf19eb40 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()
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	117
bb91bf19eb40 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:
bb91bf19eb40 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}")
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	120
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	121 # Filter for current class
bb91bf19eb40 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]
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	123
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	124 # Create the box plot
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	125 fig = plot_boxplot(
bb91bf19eb40 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'],
bb91bf19eb40 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'],
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	128 title_x='True Label',
bb91bf19eb40 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})',
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	130 )
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	131
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	132 # Save the plot
bb91bf19eb40 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(':', '_')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	134 plt.close(fig)
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	135
bb91bf19eb40 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}"
bb91bf19eb40 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')
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	138 #end if
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	139 ]]></configfile>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	140 </configfiles>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	141 <inputs>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	143 <conditional name="plot_conditional">
bb91bf19eb40 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">
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	151 </param>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	152 <when value="dimred">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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">
bb91bf19eb40 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>
bb91bf19eb40 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>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	160 </param>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	161 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	162 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	163 <when value="scatter">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	168 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	169 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	170 <when value="concordance_heatmap">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	175 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	176 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	177 <when value="pr_curve">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	180 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	181 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	182 <when value="roc_curve">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	185 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	186 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	187 <when value="box_plot">
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	190 </expand>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	191 </when>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	192 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	193 </inputs>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	194 <outputs>
bb91bf19eb40 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}: ${plot_conditional.plot_type}">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	196 <filter>plot_conditional['plot_type'] != "box_plot"</filter>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	197 </data>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	198 <collection name="boxplot_out" type="list" label="${tool.name} on ${on_string}: box_plot">
bb91bf19eb40 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/"/>
bb91bf19eb40 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>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	201 </collection>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	202 </outputs>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	203 <tests>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	204 <!-- test 1: dimred -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	207 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	215 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	216 <output name="plot_out">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	217 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	222 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	223 </output>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	224 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	225 <!-- test 2: scatter -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	228 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	235 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	236 <output name="plot_out">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	237 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	242 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	243 </output>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	244 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	245 <!-- test 3: concordance_heatmap -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	248 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	255 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	256 <output name="plot_out">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	257 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	262 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	263 </output>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	264 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	265 <!-- test 4: pr_curve -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	268 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	273 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	274 <output name="plot_out">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	275 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	280 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	281 </output>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	282 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	283 <!-- test 5: roc_curve -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	286 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	291 </conditional>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	292 <output name="plot_out">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	293 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	298 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	299 </output>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	300 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	301 <!-- test 6: box_plot -->
bb91bf19eb40 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">
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	304 <conditional name="plot_conditional">
bb91bf19eb40 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"/>
2 3c5d82bf6e8a 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 bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	309 </conditional>
bb91bf19eb40 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">
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	312 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	317 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	318 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	320 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	325 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	326 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	328 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	333 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	334 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	336 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	341 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	342 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	344 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	349 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	350 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	352 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	357 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	358 </element>
bb91bf19eb40 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">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	360 <assert_contents>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 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"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	365 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	366 </element>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	367 </output_collection>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	368 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	369 </tests>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	370 <help><![CDATA[
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	371 @COMMON_HELP@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	372
bb91bf19eb40 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.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	374
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	375 Available plot types include:
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	376
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	383
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	384
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	385 Input Files
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	386
bb91bf19eb40 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:
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	388
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 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.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	395
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	396
bb91bf19eb40 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.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	398
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	399
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	400 .. class:: warningmark
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	401
bb91bf19eb40 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!
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	403
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	404
bb91bf19eb40 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/
bb91bf19eb40 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
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	407 ]]></help>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	408 <expand macro="creator"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587 bgruening parents: diff changeset	409 <expand macro="citations"/>
bb91bf19eb40 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 @ 2:3c5d82bf6e8a draft