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comparison learner.xml @ 2:8e8569c19fa7 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 62b9598dec838ae11d6615d7b34ee5b5088c45fc
author tduigou
date Thu, 06 Feb 2025 12:49:54 +0000
parents da588cac4813
children a8e26ed8e636
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1:ee240ae47d61 2:8e8569c19fa7
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import os 8 cp '$input_param_tsv' 'param.tsv' &&
9 cp '$input_param_tsv' param.tsv && 9 mkdir 'indir' &&
10 unzip '$input_folder_zip' -d indir && 10 #for $i, $input in enumerate($input_data_csv)
11 (find indir -type f | while read file; do mv "\$file" indir; done) && 11 #if $input
12 cp '$input' 'indir/plate.${i}.csv' &&
13 #end if
14 #end for
12 python -m icfree.learner 15 python -m icfree.learner
13 --data_folder indir 16 --data_folder 'indir'
14 --parameter_file param.tsv 17 --parameter_file 'param.tsv'
15 --output_folder 'outdir' 18 --output_folder 'outdir'
16 #if str($adv.name_list) != '' 19 #if str($adv.name_list) != ''
17 --name_list '$adv.name_list' 20 --name_list '$adv.name_list'
18 #end if 21 #end if
19 #if str($adv.test) == 'true' 22 #if str($adv.test) == 'true'
34 --ks '$adv.ks' 37 --ks '$adv.ks'
35 --save_plot 38 --save_plot
36 --verbose && ls 'outdir' 39 --verbose && ls 'outdir'
37 ]]></command> 40 ]]></command>
38 <inputs> 41 <inputs>
39 <param name="input_folder_zip" type="data" format="zip" label="Zip folder containing the data files" help="Zip folder containing the data file"/> 42 <param name="input_data_csv" type="data" format="csv" multiple="true" label="Input data files" help="Input data files" />
40 <param name="input_param_tsv" type="data" format="tabular" label="Parameter values for the experiments" help="Parameter values for the experiment"/> 43 <param name="input_param_tsv" type="data" format="tabular" label="Parameter values for the experiments" help="Parameter values for the experiment"/>
41 <section name="adv" title="Advanced Options" expanded="false"> 44 <section name="adv" title="Advanced Options" expanded="false">
42 <param name="name_list" type="text" value="" label="Labels of the feature list" help="A comma-separated string of column names or identifiers, converted to a list of strings representing columns that contain labels (y). This separates y columns from the rest (X features). (Default: Yield1,Yield2,Yield3,Yield4,Yield5)" /> 45 <param name="name_list" type="text" value="" label="Labels of the feature list" help="A comma-separated string of column names or identifiers, converted to a list of strings representing columns that contain labels (y). This separates y columns from the rest (X features). (Default: Yield1,Yield2,Yield3,Yield4,Yield5)" />
43 <param name="test" type="boolean" label="Validate the model" help="A flag for validating the model; not required to run inside the active learning loop. If not set, skip the validating step" checked="false" /> 46 <param name="test" type="boolean" label="Validate the model" help="A flag for validating the model; not required to run inside the active learning loop. If not set, skip the validating step" checked="false" />
44 <param name="nb_rep" type="integer" value="100" label="Number of test repetitions for validation the model behavior" help="The number of test repetitions for validating the model behavior. 80% of data is randomly separated for training, and 20% is used for testing." /> 47 <param name="nb_rep" type="integer" value="100" label="Number of test repetitions for validation the model behavior" help="The number of test repetitions for validating the model behavior. 80% of data is randomly separated for training, and 20% is used for testing." />
64 </when> 67 </when>
65 </conditional> 68 </conditional>
66 </section> 69 </section>
67 </inputs> 70 </inputs>
68 <outputs> 71 <outputs>
69 <collection name="output_csv" type="list" label="${tool.name} - Data"> 72 <data name="output_csv" format="csv" label="${tool.name} - Data">
70 <discover_datasets pattern="(?P&lt;name&gt;.*).csv" format="csv" directory="outdir" /> 73 <!-- <discover_datasets pattern="(?P&lt;name&gt;.*).csv" ext="csv" directory="outdir" /> -->
71 </collection> 74 <discover_datasets pattern="__designation_and_ext__" ext="csv" directory="outdir" />
75 </data>
72 <collection name="output_png" type="list" label="${tool.name} - Plot"> 76 <collection name="output_png" type="list" label="${tool.name} - Plot">
73 <discover_datasets pattern="(?P&lt;name&gt;.*).png" format="png" directory="outdir" /> 77 <discover_datasets pattern="(?P&lt;name&gt;.*).png" format="png" directory="outdir" />
74 </collection> 78 </collection>
75 </outputs> 79 </outputs>
76 <tests> 80 <tests>
77 <test> 81 <test>
78 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp -save_plot -verbose -seed 85 --> 82 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp -save_plot -verbose -seed 85 -->
79 <param name="input_folder_zip" value="learner.input.folder.zip" /> 83 <param name="input_data_csv" value="learner.input.data.1.csv,learner.input.data.2.csv" />
80 <param name="input_param_tsv" value="learner.input.param.tsv" /> 84 <param name="input_param_tsv" value="learner.input.param.tsv" />
81 <output_collection name="output_csv" type="list" count="1"> 85 <output name="output_csv">
82 <element name="next_sampling_ei50" ftype="csv" > 86 <discovered_dataset designation="next_sampling_ei50" ftype="csv">
83 <assert_contents> 87 <assert_contents>
84 <has_n_lines n="51" /> 88 <has_n_lines n="51" />
85 </assert_contents> 89 </assert_contents>
86 </element> 90 </discovered_dataset>
87 </output_collection> 91 </output>
88 <output_collection name="output_png" type="list" count="4"> 92 <output_collection name="output_png" type="list" count="4">
89 <element name="EI selected"> 93 <element name="EI selected">
90 <assert_contents> 94 <assert_contents>
91 <has_size value="77k" delta="1k"/> 95 <has_size value="77k" delta="1k"/>
92 </assert_contents> 96 </assert_contents>
108 </element> 112 </element>
109 </output_collection> 113 </output_collection>
110 </test> 114 </test>
111 <test> 115 <test>
112 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp2 -name_list "Yield1,Yield2" -nb_rep 5 -flatten -seed 85 -nb_new_data_predict 20 -nb_new_data 2 -parameter_step 2 -n_group 3 -km 5 -ks 2 -save_plot -verbose --> 116 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp2 -name_list "Yield1,Yield2" -nb_rep 5 -flatten -seed 85 -nb_new_data_predict 20 -nb_new_data 2 -parameter_step 2 -n_group 3 -km 5 -ks 2 -save_plot -verbose -->
113 <param name="input_folder_zip" value="learner.input.folder.zip" /> 117 <param name="input_data_csv" value="learner.input.data.1.csv,learner.input.data.2.csv" />
114 <param name="input_param_tsv" value="learner.input.param.tsv" /> 118 <param name="input_param_tsv" value="learner.input.param.tsv" />
115 <param name="name_list" value="Yield1,Yield2" /> 119 <param name="name_list" value="Yield1,Yield2" />
116 <param name="nb_rep" value="5" /> 120 <param name="nb_rep" value="5" />
117 <param name="flatten" value="true" /> 121 <param name="flatten" value="true" />
118 <param name="nb_new_data_predict" value="20" /> 122 <param name="nb_new_data_predict" value="20" />
119 <param name="nb_new_data" value="2" /> 123 <param name="nb_new_data" value="2" />
120 <param name="parameter_step" value="2" /> 124 <param name="parameter_step" value="2" />
121 <param name="n_group" value="3" /> 125 <param name="n_group" value="3" />
122 <param name="km" value="5" /> 126 <param name="km" value="5" />
123 <param name="ks" value="2" /> 127 <param name="ks" value="2" />
124 <output_collection name="output_csv" type="list" count="1"> 128 <!-- <element name="next_sampling_ei5" file="learner.output.data.2.csv" ftype="csv" > -->
125 <element name="next_sampling_ei5" file="learner.output.data.2.csv" ftype="csv" > 129 <output name="output_csv">
130 <discovered_dataset designation="next_sampling_ei5" ftype="csv">
126 <assert_contents> 131 <assert_contents>
127 <has_n_lines n="6" /> 132 <has_n_lines n="6" />
128 </assert_contents> 133 </assert_contents>
129 </element> 134 </discovered_dataset>
130 </output_collection> 135 </output>
131 <output_collection name="output_png" type="list" count="4"> 136 <output_collection name="output_png" type="list" count="4">
132 <element name="EI selected"> 137 <element name="EI selected">
133 <assert_contents> 138 <assert_contents>
134 <has_size value="24k" delta="1k"/> 139 <has_size value="24k" delta="1k"/>
135 </assert_contents> 140 </assert_contents>