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annotate pre_process.xml @ 24:9e43ee712723 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author bgruening
date Tue, 14 May 2019 18:19:35 -0400
parents d6b8103c909c
children 685046e0381a
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1 <tool id="sklearn_data_preprocess" name="Preprocess" version="@VERSION@">
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2 <description>raw feature vectors into standardized datasets</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command>
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10 <![CDATA[
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11 python "$pre_processor_script" '$inputs'
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12 ]]>
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13 </command>
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14 <configfiles>
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15 <inputs name="inputs" />
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16 <configfile name="pre_processor_script">
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17 <![CDATA[
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18 import sys
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19 import json
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20 import pandas
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21 import pickle
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22 from scipy.io import mmread
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23 from scipy.io import mmwrite
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24 from sklearn import preprocessing
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25
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26 sys.path.insert(0, '$__tool_directory__')
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27 from utils import read_columns
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28
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29 input_json_path = sys.argv[1]
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30 with open(input_json_path, "r") as param_handler:
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31 params = json.load(param_handler)
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32
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33 #if $input_type.selected_input_type == "sparse":
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34 X = mmread("$infile")
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35 #else:
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36 header = 'infer' if params["input_type"]["header1"] else None
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37 column_option = params["input_type"]["column_selector_options_1"]["selected_column_selector_option"]
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38 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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39 c = params["input_type"]["column_selector_options_1"]["col1"]
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40 else:
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41 c = None
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42 X = read_columns(
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43 "$input_type.infile",
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44 c = c,
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45 c_option = column_option,
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46 sep='\t',
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47 header=header,
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48 parse_dates=True,
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49 encoding=None,
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50 index_col=None,
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51 tupleize_cols=False).astype(float)
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52 #end if
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53
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54 preprocessor = params["input_type"]["pre_processors"]["selected_pre_processor"]
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55 options = params["input_type"]["pre_processors"]["options"]
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56
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57 my_class = getattr(preprocessing, preprocessor)
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58 estimator = my_class(**options)
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59 estimator.fit(X)
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60 result = estimator.transform(X)
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61
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62 #if $input_type.selected_input_type == "sparse":
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63 with open("$outfile_transform", "wb") as transform_handler:
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64 mmwrite(transform_handler, result)
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65 #else:
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66 res = pandas.DataFrame(result)
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67 res.to_csv(path_or_buf = "$outfile_transform", sep="\t", index=False, header=None)
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68 #end if
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69
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70 #if $save:
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71 with open("$outfile_fit", 'wb') as out_handler:
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72 pickle.dump(estimator, out_handler, pickle.HIGHEST_PROTOCOL)
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73 #end if
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74 ]]>
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75 </configfile>
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76 </configfiles>
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77 <inputs>
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78 <conditional name="input_type">
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79 <param name="selected_input_type" type="select" label="Select the type of your input data:">
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80 <option value="tabular" selected="true">Tabular</option>
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81 <option value="sparse">Sparse</option>
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82 </param>
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83 <when value="tabular">
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84 <param name="infile" type="data" format="tabular" label="Select a tabular file you want to train your preprocessor on its data:" />
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85 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
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86 <conditional name="column_selector_options_1">
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87 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile"/>
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88 </conditional>
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89 <conditional name="pre_processors">
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90 <expand macro="sparse_preprocessors_ext" />
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91 <expand macro="sparse_preprocessor_options_ext" />
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92 </conditional>
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93 </when>
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94 <when value="sparse">
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95 <param name="infile" type="data" format="txt" label="Select a sparse representation you want to train your preprocessor on its data:"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
96 <conditional name="pre_processors">
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
97 <expand macro="sparse_preprocessors"/>
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diff changeset
98 <expand macro="sparse_preprocessor_options"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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99 </conditional>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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100 </when>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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101 </conditional>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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102 <param name="save" type="boolean" truevalue="booltrue" falsevalue="boolflase" checked="false"
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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103 label="Save the preprocessor"
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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104 help="Saves the preprocessor after fitting to the data. The preprocessor can then be passed to other tools and used in later operations."/>
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105 </inputs>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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106 <outputs>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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107 <data format="tabular" name="outfile_transform" from_work_dir="./output"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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108 <data format="zip" name="outfile_fit">
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109 <filter>save</filter>
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110 </data>
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111 </outputs>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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112 <tests>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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113 <test>
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114 <param name="infile" value="train.tabular" ftype="tabular"/>
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115 <param name="selected_column_selector_option" value="all_columns"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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116 <param name="selected_input_type" value="tabular"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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117 <param name="selected_pre_processor" value="KernelCenterer"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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118 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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119 <output name="outfile_transform" file="prp_result01" ftype="tabular"/>
23
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120 <output name="outfile_fit" file="prp_model01" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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121 </test>
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122 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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123 <param name="infile" value="train.tabular" ftype="tabular"/>
15
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124 <param name="selected_column_selector_option" value="all_columns"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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125 <param name="selected_input_type" value="tabular"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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126 <param name="selected_pre_processor" value="MinMaxScaler"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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127 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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128 <output name="outfile_transform" file="prp_result02" ftype="tabular"/>
23
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129 <output name="outfile_fit" file="prp_model02" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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130 </test>
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131 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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132 <param name="infile" value="train.tabular" ftype="tabular"/>
15
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diff changeset
133 <param name="selected_column_selector_option" value="all_columns"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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134 <param name="selected_input_type" value="tabular"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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135 <param name="selected_pre_processor" value="PolynomialFeatures"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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136 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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137 <output name="outfile_transform" file="prp_result03" ftype="tabular"/>
23
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138 <output name="outfile_fit" file="prp_model03" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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139 </test>
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140 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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141 <param name="infile" value="train.tabular" ftype="tabular"/>
15
dad38f036e83 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
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diff changeset
142 <param name="selected_column_selector_option" value="all_columns"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
143 <param name="selected_input_type" value="tabular"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
144 <param name="selected_pre_processor" value="RobustScaler"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
145 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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146 <output name="outfile_transform" file="prp_result04" ftype="tabular"/>
23
d6b8103c909c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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147 <output name="outfile_fit" file="prp_model04" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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148 </test>
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149 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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150 <param name="infile" value="csr_sparse2.mtx" ftype="txt"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
151 <param name="selected_input_type" value="sparse"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
152 <param name="selected_pre_processor" value="Binarizer"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
153 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
154 <output name="outfile_transform" file="prp_result05" ftype="tabular"/>
23
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diff changeset
155 <output name="outfile_fit" file="prp_model05" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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156 </test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
157 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
158 <param name="infile" value="csr_sparse2.mtx" ftype="txt"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
159 <param name="selected_input_type" value="sparse"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
160 <param name="selected_pre_processor" value="Imputer"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
161 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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162 <param name="axis" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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163 <output name="outfile_transform" file="prp_result06" ftype="tabular"/>
23
d6b8103c909c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
164 <output name="outfile_fit" file="prp_model06" ftype="zip" compare="sim_size" delta="50"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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165 </test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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166 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
167 <param name="infile" value="train.tabular" ftype="tabular"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
168 <param name="selected_input_type" value="tabular"/>
15
dad38f036e83 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f54ff2ba2f8e7542d68966ce5a6b17d7f624ac48
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diff changeset
169 <param name="selected_column_selector_option" value="all_columns"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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170 <param name="selected_pre_processor" value="StandardScaler"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
171 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
172 <output name="outfile_transform" file="prp_result07" ftype="tabular"/>
23
d6b8103c909c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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173 <output name="outfile_fit" file="prp_model07" ftype="zip" compare="sim_size" delta="5"/>
0
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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174 </test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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175 <test>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
176 <param name="infile" value="csr_sparse2.mtx" ftype="txt"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
177 <param name="selected_input_type" value="sparse"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
178 <param name="selected_pre_processor" value="MaxAbsScaler"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
179 <param name="save" value="true"/>
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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180 <output name="outfile_transform" file="prp_result08" ftype="tabular"/>
23
d6b8103c909c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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181 <output name="outfile_fit" file="prp_model08" ftype="zip" compare="sim_size" delta="5"/>
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182 </test>
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183 <test>
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184 <param name="infile" value="csr_sparse2.mtx" ftype="txt"/>
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185 <param name="selected_input_type" value="sparse"/>
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186 <param name="selected_pre_processor" value="Normalizer"/>
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187 <param name="save" value="true"/>
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188 <output name="outfile_transform" file="prp_result09" ftype="tabular"/>
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189 <output name="outfile_fit" file="prp_model09" ftype="zip" compare="sim_size" delta="5"/>
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190 </test>
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191 </tests>
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192 <help>
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193 <![CDATA[
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194 **What it does**
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195
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196 This tool provides several transformer classes to change raw feature vectors into a representation that is more suitable for the downstream estimators. The library is provided by sklearn.preprocessing package.
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197
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198 For information about preprocessing classes and parameter settings please refer to `Scikit-learn preprocessing`_.
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199
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200 .. _`Scikit-learn preprocessing`: http://scikit-learn.org/stable/modules/preprocessing.html
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201 ]]>
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202 </help>
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203 <expand macro="sklearn_citation"/>
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204 </tool>