Mercurial > repos > iuc > spapros_evaluation

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
author iuc
date Mon, 16 Sep 2024 11:37:34 +0000
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0
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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1 <tool id="spapros_evaluation" name="Evaluation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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2 <description>of marker genes with spapros</description>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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3 <macros>
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4 <import>macros.xml</import>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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5 </macros>
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6 <expand macro="requirements">
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7 </expand>
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8 <expand macro="version_command"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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9 <command detect_errors="exit_code"><![CDATA[
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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10 @CMD@
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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11 ]]></command>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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12 <configfiles>
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13 <configfile name="script_file"><![CDATA[
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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14 @CMD_imports@
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15 @CMD_read_inputs@
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16
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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17 mpl.rcParams['figure.dpi'] = $figure_options.dpi
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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18 plt.rcParams["font.size"] = $figure_options.fontsize
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19
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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20 header_probeset='infer'
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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21 #if $header_probeset == 'not_included':
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22 header_probeset=None
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23 #end if
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24
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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25 ## Probe set generation
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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26 probeset = pd.read_csv('$probeset', sep='\t', index_col=0, header=header_probeset)
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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27 probeset = [x for x in probeset.values.flatten().tolist() if not pd.isna(x)]
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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28
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29 ## Reference set generation
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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30 methods_pre="#echo ','.join(["%s" % $s for $i, $s in enumerate($methods_reference)])#"
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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31 methods=methods_pre.split(',')
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32
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33 reference_sets = sp.se.select_reference_probesets(
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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34 adata,
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35 n=$nreference,
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36 #if $genes_key != '':
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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37 genes_key='$genes_key',
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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38 #else:
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39 genes_key=None,
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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40 #end if
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41 #if $obs_key != '':
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42 obs_key='$obs_key',
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43 #end if
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44 #if $seeds != '':
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45 seeds=[$seeds],
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46 #end if
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47 methods=methods,
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48 verbosity=0
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49 )
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50
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51 ## Parameter setting
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52
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53 custom_params = {
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54 'data': {
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55 'name': '$probeset_name',
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56 'celltype_key': '$celltype_key'
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57 },
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58 'metrics': {
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59 #if $method.method == 'plot_summary' or $method.method == 'plot_cluster_similarity':
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60 'cluster_similarity': {
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61 'ns': [$method.ns_start, $method.ns_end],
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62 'AUC_borders': [#echo ",".join(["[%s, %s]" % ($s.auc_borders_start, $s.auc_borders_end) for $i, $s in enumerate($method.series_auc_borders)])#]
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63 },
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64 #end if
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65 #if $method.method == 'plot_summary' or $method.method == 'plot_knn_overlap':
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66 'knn_overlap': {
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67 'ks': [#echo ",".join([ "%s" % $s.k for $i, $s in enumerate($method.knn) ])#]
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68 },
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69 #end if
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70 #if $method.method == 'plot_confusion_matrix':
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71 'forest_clfs': {
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72 'ct_key': '$celltype_key',
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73 #if $method.method == 'plot_summary':
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74 'threshold': $method.forest_clfs_threshold
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75 #end if
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76 },
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77 #end if
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78 #if $method.method == 'plot_summary':
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79 #if $method.select_marker_corr.use_marker_corr == 'True':
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80 'marker_corr': {
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81 'per_celltype': $method.select_marker_corr.per_celltype,
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82 'per_marker': $method.select_marker_corr.per_marker,
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83 #if $method.select_marker_corr.select_per_celltype_min_mean.use_per_celltype_min_mean == 'True'
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84 'per_celltype_min_mean': $method.select_marker_corr.select_per_celltype_min_mean.per_celltype_min_mean,
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85 #end if
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86 #if $method.select_marker_corr.select_per_marker_min_mean.use_per_marker_min_mean == 'True'
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87 'per_marker_min_mean': $method.select_marker_corr.select_per_marker_min_mean.per_marker_min_mean
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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88 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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89 },
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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90 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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91 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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92 #if $method.method == 'plot_marker_corr':
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93 'marker_corr': {
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94 'per_celltype': $method.per_celltype,
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95 'per_marker': $method.per_marker,
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96 #if $method.select_per_celltype_min_mean.use_per_celltype_min_mean == 'True'
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97 'per_celltype_min_mean': $method.select_per_celltype_min_mean.per_celltype_min_mean,
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98 #else:
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99 'per_celltype_min_mean': None,
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100 #end if
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101 #if $method.select_per_marker_min_mean.use_per_marker_min_mean == 'True'
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102 'per_marker_min_mean': $method.select_per_marker_min_mean.per_marker_min_mean
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103 #else:
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104 'per_marker_min_mean': None
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105 #end if
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106 },
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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107 #end if
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108 #if $method.method == 'plot_summary':
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109 'gene_corr': {
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110 'threshold': $method.gene_corr_threshold
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111 }
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112 #end if
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113 }
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114 }
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115
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116 ## Setup evaluator
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117
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118 #if $method.method == 'plot_summary' or $method.method == 'plot_marker_corr':
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119
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120 header_markerset='infer'
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121 feature_marker=dict()
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122
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123 #if $method.method == 'plot_summary':
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124 #if $method.select_marker_corr.header_markerset == 'not_included' :
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125 header_markerset=None
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126 #end if
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127 feature_marker = {key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$method.select_marker_corr.markerset', sep='\t', index_col=0, header=header_markerset).to_dict(orient='index').items()}
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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128 #end if
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129 #if $method.method == 'plot_marker_corr':
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130 #if $method.header_markerset == 'not_included':
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131 header_markerset=None
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132 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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133 feature_marker = {key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$method.markerset', sep='\t', index_col=0, header=header_markerset).to_dict(orient='index').items()}
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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134 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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135
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136 #end if
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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137
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138 evaluator = sp.ev.ProbesetEvaluator(
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139 adata,
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140 metrics_params=custom_params,
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141 scheme="full",
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142 verbosity=0,
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143 #if $method.method == 'plot_summary' or $method.method == 'plot_marker_corr':
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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144 marker_list=feature_marker,
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145 #end if
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146 results_dir=None
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147 )
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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148
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149 ## Evaluation reference set
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150 for set_id, df in reference_sets.items():
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151 gene_set = df[df["selection"]].index.to_list()
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152 evaluator.evaluate_probeset(gene_set, set_id=set_id)
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153
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154 ## Evaluation probe set
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155 evaluator.evaluate_probeset(probeset, set_id='$probeset_name')
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156
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157 ## Execution of method ##
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158
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159 #if $method.method == 'plot_summary':
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160 evaluator.plot_summary(
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161 @CMD_plot@
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162 )
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163 #end if
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164
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165 #if $method.method == 'plot_confusion_matrix':
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166 evaluator.plot_confusion_matrix(
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167 @CMD_plot@
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168 )
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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169 #end if
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170
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171 #if $method.method == 'plot_coexpression':
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172 evaluator.plot_coexpression(
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173 @CMD_plot@
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174 )
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175 #end if
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176
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177 #if $method.method == 'plot_cluster_similarity':
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178 evaluator.plot_cluster_similarity(
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179 @CMD_plot@
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180 )
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181 #end if
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182
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183 #if $method.method == 'plot_knn_overlap':
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184 evaluator.plot_knn_overlap(
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185 @CMD_plot@
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186 )
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187 #end if
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188
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189 ## plot_marker_corr does not allow for the show keyword
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190 #if $method.method == 'plot_marker_corr':
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191 evaluator.plot_marker_corr(
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192 #if $method.set_ids != 'all' and $method.set_ids != '':
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193 set_ids=[$method.set_ids],
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194 #end if
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195 save='plot.$format'
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196 )
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197 #end if
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198
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199 ]]></configfile>
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200 </configfiles>
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201 <inputs>
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202 <expand macro="inputs_anndata"/>
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203 <expand macro="param_plot_format"/>
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204 <param name="probeset" type="data" format="tabular" label="Probeset tabular file with rows=conditions (e.g., celltypes) and column=features (e.g., genes)"/>
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205 <param name="header_probeset" type="select" optional="false" label="Header in the list of probes?">
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206 <option value="included">Header incldued</option>
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207 <option value="not_included">Header not included</option>
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208 </param>
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209 <param argument="nreference" type="integer" value="10" min="1" optional="false" label="Number of selected genes to generate a reference set"/>
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210 <param name="methods_reference" type="select" multiple="True" optional="false" label="Select the methods to genereate a reference probeset">
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211 <option value="random" selected="true">Random</option>
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212 <option value="PCA" selected="false">PCA</option>
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213 <option value="DE" selected="false">Differential expressed features based on wilxocon rank genes test (DE)</option>
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214 <option value="HVG" selected="false">Highly variable features (HVG)</option>
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215 </param>
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216 <param name="genes_key" type="text" optional="true" label="adata.var key for subset of preselected genes to run the selections" help="This is typically highly_variable_genes. Leave empty to not subset genes."/>
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217 <param name="obs_key" type="text" optional="true" label="Column name of adata.obs for which marker scores are calculated" help="Only required for method DE."/>
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218 <param name="seeds" type="text" optional="true" label="List of random integer seeds (comma seperated, e.g., 123,999,22)" help="For each seed, one random gene set is selected if random in methods. Leave it empty to for one random set with a random seed."/>
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219 <param name="probeset_name" type="text" value="probeset" optional="false" label="Name for your probeset that should be displayed in plots"/>
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220 <param name="celltype_key" type="text" value="celltype" optional="false" label="Column name of adata.obs that represents groups of your cells (e.g., celltype)"/>
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221 <conditional name="method">
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222 <param argument="method" type="select" optional="false" label="Method of spapros">
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223 <option value="plot_summary">Plot statistic summary, using 'evaluator.plot_summary'</option>
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224 <option value="plot_confusion_matrix">Plot confusion matrix, using 'evaluator.plot_confusion_matrix'</option>
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225 <option value="plot_coexpression">Plot coexpression heatmap, using 'evaluator.plot_coexpression'</option>
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226 <option value="plot_cluster_similarity">Plot cluster similariy, using 'evaluator.plot_cluster_similarity'</option>
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227 <option value="plot_knn_overlap">Plot knn overlap, using 'evaluator.plot_knn_overlap'</option>
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228 <option value="plot_marker_corr">Plot featue marker correlation, using 'evaluator.plot_marker_corr'</option>
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229 </param>
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230 <when value="plot_summary">
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231 <expand macro="set_ids"/>
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232 <param name="forest_clfs_threshold" type="float" value="0.8" min="0.0" max="1.0" label="Assesses how many cell types (%) can be predicted with an accuracy of at least threshold" help="The metric gives an idea about how many cell types can be identified with high confidence with the given gene set."/>
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233 <param name="gene_corr_threshold" type="float" value="0.8" min="0.0" max="1.0" label="Percentage of features (e.g., genes) that have a maximum correlation of less than threshold with all other features" help="This metric gives an idea about how many features show unique expression profiles in the gene set."/>
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234 <param name="ns_start" type="integer" value="5" min="1" label="The minimum number of leiden clusters clusters" help="Clusterings are calculated with different leiden resolutions to genertate clusterings of n = ns_start to ns_end clusters."/>
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235 <param name="ns_end" type="integer" value="21" min="1" label="The maximum number of leiden clusters clusters" help="Clusterings are calculated with different leiden resolutions to genertate clusterings of n = ns_start to ns_end clusters."/>
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236 <repeat name="series_auc_borders" title="Calculates nmi AUCs over given borders">
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237 <param name="auc_borders_start" type="integer" value="15" min="1" label="Calculates nmi over n ranges auc_borders_start to auc_borders_end" help="Defined border shouldn't exceed values in nmis."/>
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238 <param name="auc_borders_end" type="integer" value="20" min="1" label="Calculates nmi over n ranges auc_borders_start to auc_borders_end" help="Defined border shouldn't exceed values in nmis."/>
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239 </repeat>
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240 <repeat name="knn" title="Calculate knn graphs for each k">
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241 <param name="k" type="integer" value="10" min="1" label="Includes nearest neighbors for all k"/>
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242 </repeat>
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243 <conditional name="select_marker_corr">
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244 <param name="use_marker_corr" type="select" label="Do you want to calculate the correlation between your probeset and marker features?">
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245 <option value="False">No</option>
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246 <option value="True">Yes</option>
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247 </param>
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248 <when value="True">
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249 <expand macro="param_markerset"/>
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250 <param name="per_celltype" type="boolean" truevalue="True" falsevalue="False" label="Wether to return columns with per cell type max correlations" checked="true"/>
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251 <param name="per_marker" type="boolean" truevalue="True" falsevalue="False" label="Wether to return columns with per marker max correlations" checked="true"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
252 <conditional name="select_per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
253 <param name="use_per_celltype_min_mean" type="select" label="Add a column for correlation per cell type that only takes into accounts markers with mean expression > per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
254 <option value="False">No</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
255 <option value="True">Yes</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
256 </param>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
257 <when value="True">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
258 <param name="per_celltype_min_mean" type="float" value="0.0" min="0.0" label="Set per_celltype_min_mean"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
259 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
260 <when value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
261 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
262 <conditional name="select_per_marker_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
263 <param name="use_per_marker_min_mean" type="select" label="Add a column for correlation per cell type that only takes into accounts markers with mean expression > per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
264 <option value="False">No</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
265 <option value="True">Yes</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
266 </param>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
267 <when value="True">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
268 <param name="per_marker_min_mean" type="float" value="0.0" min="0.0" label="Set per_marker_min_mean"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
269 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
270 <when value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
271 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
272 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
273 <when value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
274 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
275 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
276 <when value="plot_confusion_matrix">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
277 <expand macro="set_ids"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
278 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
279 <when value="plot_coexpression">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
280 <expand macro="set_ids"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
281 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
282 <when value="plot_cluster_similarity">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
283 <expand macro="set_ids"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
284 <param name="ns_start" type="integer" value="5" min="1" label="The minimum number of leiden clusters clusters" help="Clusterings are calculated with different leiden resolutions to genertate clusterings of n = ns_start to ns_end clusters."/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
285 <param name="ns_end" type="integer" value="21" min="1" label="The maximum number of leiden clusters clusters" help="Clusterings are calculated with different leiden resolutions to genertate clusterings of n = ns_start to ns_end clusters."/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
286 <repeat name="series_auc_borders" title="Calculates nmi AUCs over given borders">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
287 <param name="auc_borders_start" type="integer" value="15" min="1" label="Calculates nmi over n ranges auc_borders_start to auc_borders_end" help="Defined border shouldn't exceed values in nmis."/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
288 <param name="auc_borders_end" type="integer" value="20" min="1" label="Calculates nmi over n ranges auc_borders_start to auc_borders_end" help="Defined border shouldn't exceed values in nmis."/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
289 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
290 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
291 <when value="plot_knn_overlap">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
292 <expand macro="set_ids"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
293 <repeat name="knn" title="Calculate knn graphs for each k">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
294 <param name="k" type="integer" value="10" min="1" label="Includes nearest neighbors for all k"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
295 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
296 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
297 <when value="plot_marker_corr">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
298 <expand macro="param_markerset"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
299 <expand macro="set_ids"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
300 <param name="per_celltype" type="boolean" truevalue="True" falsevalue="False" label="Wether to return columns with per cell type max correlations" checked="true"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
301 <param name="per_marker" type="boolean" truevalue="True" falsevalue="False" label="Wether to return columns with per marker max correlations" checked="true"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
302 <conditional name="select_per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
303 <param name="use_per_celltype_min_mean" type="select" label="Add a column for correlation per cell type that only takes into accounts markers with mean expression > per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
304 <option value="False">No</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
305 <option value="True">Yes</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
306 </param>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
307 <when value="True">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
308 <param name="per_celltype_min_mean" type="float" value="0.0" min="0.0" label="Set per_celltype_min_mean"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
309 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
310 <when value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
311 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
312 <conditional name="select_per_marker_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
313 <param name="use_per_marker_min_mean" type="select" label="Add a column for correlation per cell type that only takes into accounts markers with mean expression > per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
314 <option value="False">No</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
315 <option value="True">Yes</option>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
316 </param>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
317 <when value="True">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
318 <param name="per_marker_min_mean" type="float" value="0.0" min="0.0" label="Set per_marker_min_mean"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
319 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
320 <when value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
321 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
322 </when>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
323 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
324 <section name="figure_options" title="Figure Output Options" expanded="false">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
325 <param argument="dpi" type="integer" value="300" min="1" label="Dpi of figures"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
326 <param argument="fontsize" type="integer" value="100" min="1" label="Font size of figures"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
327 </section>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
328 <expand macro="inputs_common_advanced"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
329 </inputs>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
330 <outputs>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
331 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
332 <filter>format == 'png'</filter>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
333 </data>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
334 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
335 <filter>format == 'pdf'</filter>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
336 </data>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
337 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
338 <filter>format == 'svg'</filter>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
339 </data>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
340 <expand macro="hidden_outputs"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
341 </outputs>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
342 <tests>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
343 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
344 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
345 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
346 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
347 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
348 <param name="nreference" value="30"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
349 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
350 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
351 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
352 <param name="seeds" value="123,124"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
353 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
354 <param name="method" value="plot_summary"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
355 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
356 <param name="forest_clfs_threshold" value="0.8"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
357 <param name="gene_corr_threshold" value="0.8"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
358 <param name="ns_start" value="5"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
359 <param name="ns_end" value="21"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
360 <repeat name="series_auc_borders">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
361 <param name="auc_borders_start" value="7"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
362 <param name="auc_borders_end" value="14"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
363 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
364 <repeat name="series_auc_borders">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
365 <param name="auc_borders_start" value="15"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
366 <param name="auc_borders_end" value="20"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
367 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
368 <repeat name="knn">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
369 <param name="k" value="5"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
370 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
371 <repeat name="knn">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
372 <param name="k" value="10"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
373 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
374 <conditional name="select_marker_corr">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
375 <param name="use_marker_corr" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
376 <param name="markerset" value="marker.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
377 <param name="header_markerset" value="not_included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
378 <param name="per_celltype" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
379 <param name="per_marker" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
380 <conditional name="select_per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
381 <param name="use_per_celltype_min_mean" value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
382 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
383 <conditional name="select_per_marker_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
384 <param name="use_per_marker_min_mean" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
385 <param name="per_marker_min_mean" value="0.025"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
386 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
387 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
388 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
389 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
390 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
391 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
392 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
393 <has_text_matching expression="'per_celltype': True,"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
394 <has_text_matching expression="'per_marker': True,"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
395 <has_text_matching expression="'per_marker_min_mean': 0.025"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
396 <has_text_matching expression="evaluator.plot_summary"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
397 <has_text_matching expression="save='plot.png',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
398 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
399 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
400 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
401 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
402 <has_image_width width="3253" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
403 <has_image_height height="1446" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
404 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
405 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
406 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
407 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
408 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
409 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
410 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
411 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
412 <param name="nreference" value="30"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
413 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
414 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
415 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
416 <param name="seeds" value="123,124"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
417 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
418 <param name="method" value="plot_confusion_matrix"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
419 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
420 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
421 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
422 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
423 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
424 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
425 <has_text_matching expression="'ct_key': 'celltype',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
426 <has_text_matching expression="evaluator.plot_confusion_matrix"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
427 <has_text_matching expression="save='plot.png',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
428 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
429 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
430 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
431 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
432 <has_image_width width="4560" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
433 <has_image_height height="1859" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
434 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
435 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
436 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
437 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
438 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
439 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
440 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
441 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
442 <param name="nreference" value="30"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
443 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
444 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
445 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
446 <param name="seeds" value="123,124"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
447 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
448 <param name="method" value="plot_coexpression"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
449 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
450 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
451 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
452 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
453 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
454 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
455 <has_text_matching expression="evaluator.plot_coexpression"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
456 <has_text_matching expression="save='plot.png',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
457 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
458 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
459 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
460 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
461 <has_image_width width="5412" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
462 <has_image_height height="3463" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
463 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
464 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
465 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
466 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
467 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
468 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
469 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
470 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
471 <param name="nreference" value="30"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
472 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
473 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
474 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
475 <param name="seeds" value="123,124"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
476 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
477 <param name="method" value="plot_cluster_similarity"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
478 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
479 <param name="ns_start" value="3"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
480 <param name="ns_end" value="20"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
481 <repeat name="series_auc_borders">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
482 <param name="auc_borders_start" value="7"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
483 <param name="auc_borders_end" value="14"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
484 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
485 <repeat name="series_auc_borders">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
486 <param name="auc_borders_start" value="15"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
487 <param name="auc_borders_end" value="20"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
488 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
489 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
490 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
491 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
492 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
493 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
494 <has_text_matching expression="evaluator.plot_cluster_similarity"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
495 <has_text_matching expression="save='plot.png',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
496 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
497 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
498 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
499 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
500 <has_image_width width="3223" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
501 <has_image_height height="1406" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
502 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
503 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
504 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
505 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
506 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
507 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
508 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
509 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
510 <param name="nreference" value="30"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
511 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
512 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
513 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
514 <param name="seeds" value="123,124"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
515 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
516 <param name="method" value="plot_knn_overlap"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
517 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
518 <repeat name="knn">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
519 <param name="k" value="6"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
520 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
521 <repeat name="knn">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
522 <param name="k" value="11"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
523 </repeat>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
524 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
525 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
526 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
527 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
528 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
529 <has_text_matching expression="evaluator.plot_knn_overlap"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
530 <has_text_matching expression="save='plot.png',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
531 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
532 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
533 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
534 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
535 <has_image_width width="3223" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
536 <has_image_height height="1406" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
537 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
538 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
539 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
540 <test expect_num_outputs="2">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
541 <param name="adata" value="tl.rank_genes_groups.newton-cg.pbmc68k_reduced_240cells.h5ad"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
542 <param name="format" value="png"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
543 <param name="probeset" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
544 <param name="header_probeset" value="included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
545 <param name="nreference" value="50"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
546 <param name="methods_reference" value="random,PCA,DE,HVG"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
547 <param name="genes_key" value="highly_variable"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
548 <param name="obs_key" value="celltype"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
549 <conditional name="method">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
550 <param name="method" value="plot_marker_corr"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
551 <param name="set_ids" value="all"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
552 <param name="use_marker_corr" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
553 <param name="markerset" value="marker.tsv"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
554 <param name="header_markerset" value="not_included"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
555 <param name="per_celltype" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
556 <param name="per_marker" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
557 <conditional name="select_per_celltype_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
558 <param name="use_per_celltype_min_mean" value="False"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
559 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
560 <conditional name="select_per_marker_min_mean">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
561 <param name="use_per_marker_min_mean" value="True"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
562 <param name="per_marker_min_mean" value="0.025"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
563 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
564 </conditional>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
565 <param name="show_log" value="true" />
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
566 <output name="hidden_output">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
567 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
568 <has_text_matching expression="'name': 'probeset',"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
569 <has_text_matching expression="'per_celltype': True,"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
570 <has_text_matching expression="'per_marker': True,"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
571 <has_text_matching expression="'per_marker_min_mean': 0.025"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
572 <has_text_matching expression="evaluator.plot_marker_corr"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
573 <has_text_matching expression="save='plot.png'"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
574 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
575 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
576 <output name="out_png">
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
577 <assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
578 <has_image_width width="5064" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
579 <has_image_height height="4554" delta="2"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
580 </assert_contents>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
581 </output>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
582 </test>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
583 </tests>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
584 <help><![CDATA[
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
585 Probe set evaluation for single-cell sequencing data using spapros.
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
586 ============================================================================================================
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
iuc
parents:
diff changeset
587
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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588 Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data.
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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589
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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590 Key Features:
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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591 * Select probe sets for spatial transcriptomics which identify cell types of interest, capture general transcriptomic variation, and incorporate prior knowledge
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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592 * Evaluate probe sets with an extensive pipeline
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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593
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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594 Further documentation can be found here: https://spapros.readthedocs.io/en/latest/index.html.
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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595
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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596 ]]></help>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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597 <expand macro="citations"/>
0c1b0a3b19df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spapros/ commit aed7fe13fa0ed09d77a31eeecaf3ec3fba7eed3b
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598 </tool>