Mercurial > repos > ebi-gxa > celltypist_predict

annotate celltypist_CLI.py @ 1:df005630100e draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4dd95e3e6c059cc9df47f5d08e4f3f8b618830f1-dirty
author ebi-gxa
date Wed, 19 Feb 2025 12:10:17 +0000
parents a7d6985ba791
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a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
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1 import argparse
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
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2 import os
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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3 import pickle
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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4 import sys
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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5 import textwrap
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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6
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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7 import celltypist
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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8 import scanpy as sc
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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9
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10
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11 def train(
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12 input_path,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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13 labels,
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14 genes,
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15 model_name,
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16 output_path,
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17 transpose_input,
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18 normalize,
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19 raw_counts_layer,
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20 gene_symbols_field,
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21 epochs,
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22 max_iter,
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23 C,
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24 n_jobs,
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25 use_SGD,
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26 alpha,
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27 use_GPU,
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28 mini_batch,
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29 batch_number,
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30 batch_size,
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31 balance_cell_type,
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32 feature_selection,
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33 top_genes,
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34 ):
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35 """
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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36 Method used to train a CellTypist model and output the model to a desired
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37 location. Please refer to the CLI help to gain a better understanding of
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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38 the required and optional parameters.
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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39 """
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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40 if input_path.endswith(".h5ad"):
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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41 print("Detected an AnnData object as input.")
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42 data = sc.read_h5ad(input_path)
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
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43 elif input_path.endswith(".mtx"):
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44 print("Detected .mtx file as input.")
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45 data = input_path
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46 else:
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47 raise ValueError("Invalid input file type detected.")
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48 if input_path.endswith(".mtx") and genes is None:
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49 raise ValueError("Missing a gene file for the provided data.")
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50 if (
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51 raw_counts_layer
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52 and input_path.endswith(".h5ad")
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53 and raw_counts_layer in data.layers.keys()
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54 and raw_counts_layer != "X"
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55 ):
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56 print(f"Using raw counts layer: {raw_counts_layer}")
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57 data.X = data.layers[raw_counts_layer]
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58 elif raw_counts_layer and input_path.endswith(".h5ad"):
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59 raise ValueError(
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60 f"Raw counts layer {raw_counts_layer} \
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61 should be either different to 'X' or an \
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62 existing layer in AnnData"
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63 )
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64 elif raw_counts_layer:
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65 raise ValueError(
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66 f"Raw counts layer {raw_counts_layer} provided but \
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67 the data format provided is .mtx. Please provide an \
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68 AnnData object."
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69 )
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70 if (
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71 gene_symbols_field
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72 and input_path.endswith(".h5ad")
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73 and gene_symbols_field in data.var.columns
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74 ):
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75 data.var["old_index"] = data.var.index
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76 data.var.set_index(gene_symbols_field, inplace=True)
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77 if normalize:
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78 sc.pp.normalize_total(data, target_sum=1e4)
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79 sc.pp.log1p(data)
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80
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81 model = celltypist.train(
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82 data,
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83 labels=labels,
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84 genes=genes,
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85 transpose_input=transpose_input,
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86 C=C,
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87 epochs=epochs,
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88 max_iter=max_iter,
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89 n_jobs=n_jobs,
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diff changeset
90 use_SGD=use_SGD,
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91 alpha=alpha,
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92 use_GPU=use_GPU,
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93 mini_batch=mini_batch,
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diff changeset
94 batch_number=batch_number,
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95 batch_size=batch_size,
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96 balance_cell_type=balance_cell_type,
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diff changeset
97 feature_selection=feature_selection,
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98 top_genes=top_genes,
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diff changeset
99 )
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diff changeset
100
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101 model_save_location = output_path + "/" + model_name + ".pkl"
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102
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103 return pickle.dump(model, open(model_save_location, "wb"))
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104
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ebi-gxa
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diff changeset
105
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106 def predict(
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107 input_path,
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diff changeset
108 model,
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109 output_path,
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110 gene_file,
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111 cell_file,
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112 raw_counts_layer,
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113 gene_symbols_field,
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114 normalize,
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115 transpose_input,
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116 mode,
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117 p_thres,
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118 majority_voting,
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119 over_clustering,
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120 use_GPU,
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121 ):
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122 """
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123 Method used to obtain cell type prediction on a new dataset using an \
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124 existing CellTypist model.
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125 Please refer to the CLI help to gain a better understanding of the \
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126 required and optional
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127 parameters.
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128 """
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129 if input_path.endswith(".h5ad"):
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130 print("Detected an AnnData object as input.")
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131 data = sc.read_h5ad(input_path)
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132 elif input_path.endswith(".mtx"):
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133 print("Detected .mtx file as input.")
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134 data = input_path
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135 else:
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136 raise ValueError("Invalid input file type detected.")
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137 if input_path.endswith(".mtx") and gene_file is None:
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138 raise ValueError("Missing a gene file for the provided .mtx data.")
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139 if input_path.endswith(".mtx") and cell_file is None:
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140 raise ValueError("Missing a cell file for the provided .mtx data.")
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141 if (
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142 raw_counts_layer
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143 and input_path.endswith(".h5ad")
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144 and raw_counts_layer in data.layers.keys()
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145 and raw_counts_layer != "X"
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146 ):
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147 print(f"Using raw counts layer: {raw_counts_layer}")
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148 data.X = data.layers[raw_counts_layer]
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149 elif raw_counts_layer and input_path.endswith(".h5ad"):
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150 raise ValueError(
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151 f"Raw counts layer {raw_counts_layer} should be \
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152 either different to 'X' or an existing layer in \
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153 AnnData"
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154 )
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155 elif raw_counts_layer:
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156 raise ValueError(
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157 f"Raw counts layer {raw_counts_layer} provided but \
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158 the data format is .mtx. Please provide an AnnData \
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159 object."
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160 )
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161 if (
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162 gene_symbols_field
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163 and input_path.endswith(".h5ad")
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164 and gene_symbols_field in data.var.columns
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165 ):
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166 data.var["old_index"] = data.var.index
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167 data.var.set_index(gene_symbols_field, inplace=True)
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168 if normalize:
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169 sc.pp.normalize_total(data, target_sum=1e4)
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170 sc.pp.log1p(data)
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171 if mode:
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172 mode = mode.replace("_", " ")
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173 if majority_voting:
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174 if over_clustering:
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175 over_clustering = over_clustering
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176 else:
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177 over_clustering = None
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178
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179 predictions = celltypist.annotate(
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180 data,
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181 model,
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182 gene_file=gene_file,
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183 cell_file=cell_file,
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184 mode=mode,
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185 p_thres=p_thres,
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186 transpose_input=transpose_input,
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187 majority_voting=majority_voting,
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188 over_clustering=over_clustering,
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189 use_GPU=use_GPU,
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190 )
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191
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192 return predictions.predicted_labels.to_csv(output_path, sep="\t")
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193
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194
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195 def main():
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196 parser = argparse.ArgumentParser(
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197 add_help=False,
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198 description=textwrap.dedent(
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199 """
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200 CellTypist for automatic cell type annotation.
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201 ----------------------------------------------
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202 Welcome to the ODS CLI tool for cell type
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203 annotation using CellTypist.
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204 The CLI provides the user with the opportunity
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205 to train a new model or predict using an
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206 existing model.
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207 Either of the methods can be activated by
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208 providing the appropriate action variable.
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209 For details of required/optional parameters
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210 for each method, please refer to the
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211 appropriate help function (-h).
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212 """
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213 ),
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214 formatter_class=argparse.RawTextHelpFormatter,
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215 )
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216
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217 choices_to = {
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218 "train": "⚖️ Train a CellTypist model using a reference \
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219 dataset.",
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220 "predict": "🖋️ Use an existing CellTypist model to predict \
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221 on a new dataset.",
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222 }
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223
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224 parser.add_argument(
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225 "--action",
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226 type=str,
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227 help="\n".join(
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228 "{}: {}".format(key, value) for key, value in choices_to.items()
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229 ),
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230 choices=choices_to,
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231 )
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232
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233 parser.add_argument(
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234 "--help",
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235 action="store_true",
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236 help="List available options.",
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237 required=False,
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238 )
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239
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240 args, sub_args = parser.parse_known_args()
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241 if args.help:
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242 if args.action is None:
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243 print(parser.format_help())
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244 sys.exit(1)
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245 sub_args.append("--help")
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246
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247 action = "predict" if args.action is None else args.action
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248
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249 parser = argparse.ArgumentParser(
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250 prog="%s %s" % (os.path.basename(sys.argv[0]), action)
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251 )
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252
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253 if action == "predict":
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254 parser.add_argument(
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255 "--input_path",
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256 type=str,
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257 help="Path to the input file. \
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258 Can be an AnnData object or a .mtx file.",
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259 required=True,
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260 )
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261
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262 parser.add_argument(
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263 "--output_path",
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264 type=str,
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265 help="Path to output file.",
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266 required=True,
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267 )
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268
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parents:
diff changeset
269 parser.add_argument(
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parents:
diff changeset
270 "--model",
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parents:
diff changeset
271 type=str,
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parents:
diff changeset
272 help="Path to model file, stored in .pkl format.",
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parents:
diff changeset
273 required=True,
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parents:
diff changeset
274 )
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parents:
diff changeset
275
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parents:
diff changeset
276 parser.add_argument(
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parents:
diff changeset
277 "--gene_file",
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ebi-gxa
parents:
diff changeset
278 type=str,
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ebi-gxa
parents:
diff changeset
279 help=(
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parents:
diff changeset
280 "Path to the file which stores each gene \
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ebi-gxa
parents:
diff changeset
281 per line corresponding to the genes used \
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ebi-gxa
parents:
diff changeset
282 in the provided .mtx file."
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diff changeset
283 ),
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ebi-gxa
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diff changeset
284 required=False,
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ebi-gxa
parents:
diff changeset
285 default=None,
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ebi-gxa
parents:
diff changeset
286 )
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ebi-gxa
parents:
diff changeset
287
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ebi-gxa
parents:
diff changeset
288 parser.add_argument(
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ebi-gxa
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diff changeset
289 "--cell_file",
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ebi-gxa
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diff changeset
290 type=str,
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ebi-gxa
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diff changeset
291 help="Path to the file which stores each cell \
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ebi-gxa
parents:
diff changeset
292 per line corresponding to the cells used \
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ebi-gxa
parents:
diff changeset
293 in the provided .mtx file.",
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diff changeset
294 required=False,
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diff changeset
295 default=None,
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diff changeset
296 )
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ebi-gxa
parents:
diff changeset
297
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ebi-gxa
parents:
diff changeset
298 parser.add_argument(
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ebi-gxa
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diff changeset
299 "--raw_counts_layer",
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ebi-gxa
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diff changeset
300 type=str,
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ebi-gxa
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diff changeset
301 help="The name of the layer that stores the raw \
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ebi-gxa
parents:
diff changeset
302 counts. Uses default matrix if not present.",
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ebi-gxa
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diff changeset
303 required=False,
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diff changeset
304 default=None,
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ebi-gxa
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diff changeset
305 )
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ebi-gxa
parents:
diff changeset
306
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ebi-gxa
parents:
diff changeset
307 parser.add_argument(
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ebi-gxa
parents:
diff changeset
308 "--gene_symbols_field",
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ebi-gxa
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diff changeset
309 type=str,
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ebi-gxa
parents:
diff changeset
310 help="The field in AnnData where the gene symbols \
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ebi-gxa
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diff changeset
311 are stored, if not in index.",
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ebi-gxa
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diff changeset
312 required=False,
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ebi-gxa
parents:
diff changeset
313 default=None,
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ebi-gxa
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diff changeset
314 )
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ebi-gxa
parents:
diff changeset
315
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ebi-gxa
parents:
diff changeset
316 parser.add_argument(
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ebi-gxa
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diff changeset
317 "--normalize",
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ebi-gxa
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diff changeset
318 action="store_true",
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ebi-gxa
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diff changeset
319 help="If raw counts are provided in the AnnData \
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ebi-gxa
parents:
diff changeset
320 object, they need to be normalized.",
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ebi-gxa
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321 required=False,
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diff changeset
322 )
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ebi-gxa
parents:
diff changeset
323
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ebi-gxa
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diff changeset
324 parser.add_argument(
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ebi-gxa
parents:
diff changeset
325 "--transpose_input",
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ebi-gxa
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diff changeset
326 action="store_true",
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ebi-gxa
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diff changeset
327 help="If the provided matrix is in the \
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ebi-gxa
parents:
diff changeset
328 gene-by-cell format, please transpose the \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
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diff changeset
329 input to cell-by-gene format",
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ebi-gxa
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330 required=False,
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ebi-gxa
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diff changeset
331 )
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ebi-gxa
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diff changeset
332
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ebi-gxa
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diff changeset
333 parser.add_argument(
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ebi-gxa
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334 "--mode",
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ebi-gxa
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diff changeset
335 type=str,
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ebi-gxa
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336 choices=["best_match", "prob_match"],
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ebi-gxa
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337 help="Choose the cell type with the largest score/probability \
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ebi-gxa
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338 as the final prediction (`best_match`), or enable a \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
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339 multi-label classification (`prob_match`), which assigns \
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ebi-gxa
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340 0 (i.e., unassigned), 1, or >=2 cell type labels to each \
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ebi-gxa
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341 query cell. [default: best_match]",
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342 required=False,
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343 default="best_match",
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ebi-gxa
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344 )
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diff changeset
345
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ebi-gxa
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346 parser.add_argument(
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ebi-gxa
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diff changeset
347 "--p_thres",
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ebi-gxa
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348 type=float,
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ebi-gxa
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diff changeset
349 help="Probability threshold for assigning a cell \
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ebi-gxa
parents:
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350 type in a multiclass problem, defaults \
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ebi-gxa
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diff changeset
351 to 0.5.",
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ebi-gxa
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352 default=0.5,
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ebi-gxa
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diff changeset
353 required=False,
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ebi-gxa
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354 )
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ebi-gxa
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355
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ebi-gxa
parents:
diff changeset
356 parser.add_argument(
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ebi-gxa
parents:
diff changeset
357 "--majority_voting",
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ebi-gxa
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358 action="store_true",
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ebi-gxa
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diff changeset
359 help="Refine the predicted labels by running the \
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ebi-gxa
parents:
diff changeset
360 majority voting classifier after \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
361 over-clustering.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
362 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
363 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
364
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
365 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
366 "--over_clustering",
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ebi-gxa
parents:
diff changeset
367 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
368 help="If majority voting is set to True, specify \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
369 the type of over clustering that is to be \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
370 performend. This can be specified in the \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
371 AnnData or an input file specifying the \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
372 over-clustering per cell. If not present, \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
373 then the default heuristic over-clustring \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
374 based on input data will be used.",
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ebi-gxa
parents:
diff changeset
375 required=False,
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ebi-gxa
parents:
diff changeset
376 default=None,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
377 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
378
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
379 parser.add_argument(
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ebi-gxa
parents:
diff changeset
380 "--use_GPU",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
381 action="store_true",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
382 help="Whether to use GPU for over clustering \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
383 on the basis of `rapids-singlecell`.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
384 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
385 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
386
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
387 args = parser.parse_args(sub_args)
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
388
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
389 predict(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
390 args.input_path,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
391 args.model,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
392 args.output_path,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
393 args.gene_file,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
394 args.cell_file,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
395 args.raw_counts_layer,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
396 args.gene_symbols_field,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
397 args.normalize,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
398 args.transpose_input,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
399 args.mode,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
400 args.p_thres,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
401 args.majority_voting,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
402 args.over_clustering,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
403 args.use_GPU,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
404 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
405 else:
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
406 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
407 "--input_path",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
408 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
409 help="Path to the input file. Can be an\
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
410 AnnData object or a .mtx file.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
411 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
412 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
413
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
414 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
415 "--labels",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
416 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
417 help="Path to the file that stores the per cell types\
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
418 or the layer in the AnnData object where the\
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
419 cell types are held.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
420 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
421 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
422
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
423 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
424 "--genes",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
425 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
426 help="Path to the file containing one gene per line corresponding \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
427 to the genes in X, required for .mtx data.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
428 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
429 default=None,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
430 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
431
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
432 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
433 "--model_name",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
434 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
435 help="The name of the trained model, used for saving.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
436 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
437 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
438
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
439 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
440 "--output_path",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
441 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
442 help="The location to where the trained model should be saved.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
443 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
444 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
445
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
446 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
447 "--transpose_input",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
448 action="store_true",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
449 help="If the provided matrix is in the gene-by-cell format, \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
450 please transpose the input to cell-by-gene format.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
451 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
452 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
453
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
454 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
455 "--normalize",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
456 action="store_true",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
457 help="If raw counts are provided in the AnnData object, \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
458 they need to be normalized.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
459 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
460 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
461
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
462 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
463 "--gene_symbols_field",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
464 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
465 help="The field in AnnData where the gene symbols are stored, \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
466 if not in index.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
467 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
468 default=None,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
469 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
470
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
471 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
472 "--raw_counts_layer",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
473 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
474 help="The name of the layer that stores the raw counts. \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
475 Uses default matrix if not present",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
476 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
477 default=None,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
478 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
479
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
480 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
481 "--epochs",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
482 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
483 help="The number of epochs for which the model \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
484 needs to be trained.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
485 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
486 default=10,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
487 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
488
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
489 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
490 "--solver",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
491 type=str,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
492 help="Algorithm to use in the optimization problem for \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
493 traditional logistic classifier. Default is based \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
494 on the size of the input data.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
495 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
496 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
497
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
498 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
499 "--max_iter",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
500 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
501 help="Maximum number of iterations before reaching \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
502 the minimum of the cost function.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
503 required=True,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
504 default=100,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
505 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
506
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
507 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
508 "--C",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
509 type=float,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
510 help="Inverse of L2 regularization strength for \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
511 traditional logistic classifier.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
512 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
513 default=1.0,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
514 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
515
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
516 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
517 "--n_jobs",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
518 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
519 help="Number of CPUs used.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
520 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
521 default=1,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
522 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
523
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
524 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
525 "--use_SGD",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
526 type=bool,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
527 help="Whether to implement SGD learning \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
528 for the logistic classifier.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
529 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
530 default=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
531 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
532
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
533 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
534 "--alpha",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
535 type=float,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
536 help="L2 regularization strength for SGD logistic classifier.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
537 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
538 default=0.0001,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
539 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
540
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
541 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
542 "--use_GPU",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
543 type=bool,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
544 help="Whether to use GPU for logistic classifier.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
545 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
546 default=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
547 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
548
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
549 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
550 "--mini_batch",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
551 type=bool,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
552 help="Whether to implement mini-batch training \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
553 for the SGD logistic classifier.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
554 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
555 default=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
556 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
557
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
558 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
559 "--batch_number",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
560 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
561 help="The number of batches used for training in each epoch. \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
562 Each batch contains batch_size cells.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
563 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
564 default=100,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
565 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
566
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
567 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
568 "--batch_size",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
569 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
570 help="The number of cells within each batch.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
571 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
572 default=1000,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
573 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
574
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
575 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
576 "--balance_cell_type",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
577 type=bool,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
578 help="Whether to balance the cell type frequencies \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
579 in mini-batches during each epoch.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
580 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
581 default=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
582 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
583
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
584 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
585 "--feature_selection",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
586 type=bool,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
587 help="Whether to perform two-pass data training where \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
588 the first round is used for selecting important \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
589 features/genes using SGD learning.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
590 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
591 default=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
592 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
593
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
594 parser.add_argument(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
595 "--top_genes",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
596 type=int,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
597 help="The number of top genes selected from each \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
598 class/cell-type based on their absolute \
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
599 regression coefficients.",
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
600 required=False,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
601 default=300,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
602 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
603
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
604 args = parser.parse_args(sub_args)
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
605
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
606 train(
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
607 args.input_path,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
608 args.labels,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
609 args.genes,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
610 args.model_name,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
611 args.output_path,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
612 args.transpose_input,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
613 args.normalize,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
614 args.raw_counts_layer,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
615 args.gene_symbols_field,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
616 args.epochs,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
617 args.max_iter,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
618 args.C,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
619 args.n_jobs,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
620 args.use_SGD,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
621 args.alpha,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
622 args.use_GPU,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
623 args.mini_batch,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
624 args.batch_number,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
625 args.batch_size,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
626 args.balance_cell_type,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
627 args.feature_selection,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
628 args.top_genes,
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
629 )
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
630
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
631
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
632 if __name__ == "__main__":
a7d6985ba791 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 53651c0be9daeebb0921f3b5e542323304dfdc98-dirty
ebi-gxa
parents:
diff changeset
633 main()