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comparison learner.xml @ 9:9852c2c641b2 draft default tip

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 16315dee62caf50b1820964b0536c1cf61c67ceb
author tduigou
date Fri, 07 Feb 2025 11:08:31 +0000
parents fad19e8ec225
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8:fad19e8ec225 9:9852c2c641b2
40 ]]></command> 40 ]]></command>
41 <environment_variables> 41 <environment_variables>
42 <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable> 42 <environment_variable name="MPLCONFIGDIR">.matplotlib</environment_variable>
43 </environment_variables> 43 </environment_variables>
44 <inputs> 44 <inputs>
45 <param name="input_data_csv" type="data" format="csv" multiple="true" label="Input data files" help="Input data files" /> 45 <param name="input_param_tsv" type="data" format="tabular" label="Sampling file (X)"/>
46 <param name="input_param_tsv" type="data" format="tabular" label="Parameter values for the experiments" help="Parameter values for the experiment"/> 46 <param name="input_data_csv" type="data" format="csv" multiple="true" label="Fluo/Lumi values (Y)" />
47 <section name="adv" title="Advanced Options" expanded="false"> 47 <section name="adv" title="Advanced Options" expanded="false">
48 <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)" /> 48 <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)" />
49 <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" /> 49 <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" />
50 <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." /> 50 <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." />
51 <param name="flatten" type="boolean" label="Flattent feature data" help="A flag to indicate whether to flatten Y data. If set, treats each repetition in the same experiment independently; multiple same X values with different y outputs are modeled. Else, calculates the average of y across repetitions and only model with y average." /> 51 <param name="flatten" type="boolean" label="Flattent feature data" help="A flag to indicate whether to flatten Y data. If set, treats each repetition in the same experiment independently; multiple same X values with different y outputs are modeled. Else, calculates the average of y across repetitions and only model with y average." />
70 </when> 70 </when>
71 </conditional> 71 </conditional>
72 </section> 72 </section>
73 </inputs> 73 </inputs>
74 <outputs> 74 <outputs>
75 <data name="output_csv" format="csv" label="${tool.name} - Data"> 75 <data name="output_csv" format="csv" label="${tool.name} - Samples to test">
76 <discover_datasets pattern="(?P&lt;designation&gt;.*).csv" ext="csv" directory="outdir" assign_primary_output="true" /> 76 <discover_datasets pattern="(?P&lt;designation&gt;.*).csv" ext="csv" directory="outdir" assign_primary_output="true" />
77 <!-- <discover_datasets pattern="__designation_and_ext__" ext="csv" directory="outdir" assign_primary_output="true"/> --> 77 <!-- <discover_datasets pattern="__designation_and_ext__" ext="csv" directory="outdir" assign_primary_output="true"/> -->
78 </data> 78 </data>
79 <collection name="output_png" type="list" label="${tool.name} - Plot"> 79 <collection name="output_png" type="list" label="${tool.name} - Plot">
80 <discover_datasets pattern="(?P&lt;name&gt;.*).png" format="png" directory="outdir" /> 80 <discover_datasets pattern="(?P&lt;name&gt;.*).png" format="png" directory="outdir" />
83 <tests> 83 <tests>
84 <test> 84 <test>
85 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp -save_plot -verbose -seed 85 --> 85 <!-- python -m icfree.learner -data_folder learner -parameter_file learner.input.param.tsv -output_folder tmp -save_plot -verbose -seed 85 -->
86 <param name="input_data_csv" value="learner.input.data.1.csv,learner.input.data.2.csv" /> 86 <param name="input_data_csv" value="learner.input.data.1.csv,learner.input.data.2.csv" />
87 <param name="input_param_tsv" value="learner.input.param.tsv" /> 87 <param name="input_param_tsv" value="learner.input.param.tsv" />
88 <output name="output_csv"> 88 <output name="output_csv" count="1">
89 <assert_contents> 89 <assert_contents>
90 <has_n_lines n="51" /> 90 <has_n_lines n="51" />
91 </assert_contents> 91 </assert_contents>
92 </output> 92 </output>
93 <output_collection name="output_png" type="list" count="4"> 93 <output_collection name="output_png" type="list" count="4">
125 <param name="parameter_step" value="2" /> 125 <param name="parameter_step" value="2" />
126 <param name="n_group" value="3" /> 126 <param name="n_group" value="3" />
127 <param name="km" value="5" /> 127 <param name="km" value="5" />
128 <param name="ks" value="2" /> 128 <param name="ks" value="2" />
129 <!-- <element name="next_sampling_ei5" file="learner.output.data.2.csv" ftype="csv" > --> 129 <!-- <element name="next_sampling_ei5" file="learner.output.data.2.csv" ftype="csv" > -->
130 <output name="output_csv"> 130 <output name="output_csv" count="1">
131 <assert_contents> 131 <assert_contents>
132 <has_n_lines n="6" /> 132 <has_n_lines n="6" />
133 </assert_contents> 133 </assert_contents>
134 </output> 134 </output>
135 <output_collection name="output_png" type="list" count="4"> 135 <output_collection name="output_png" type="list" count="4">