Mercurial > repos > tduigou > icfree_sampler

comparison sampler.xml @ 4:fe4c1eccb687 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 79b4751f34792a1a346ada38f7b6f64571dd51e9
author tduigou
date Thu, 09 Mar 2023 16:46:15 +0000
parents d919d5c6f458
children b2dba600eb2b
comparison
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3:326935d82075 4:fe4c1eccb687
19 #end if 19 #end if
20 --nb-sampling-steps '$adv.nb_sampling_steps' 20 --nb-sampling-steps '$adv.nb_sampling_steps'
21 --nb-samples '$adv.nb_samples' 21 --nb-samples '$adv.nb_samples'
22 --seed '0' 22 --seed '0'
23 --output-format 'tsv' 23 --output-format 'tsv'
24 --output-folder . 24 --output-folder . &&
25 mv sampling.tsv '$output_sampling'
25 ]]></command> 26 ]]></command>
26 <inputs> 27 <inputs>
27 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" /> 28 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" />
28 <section name="adv" title="Advanced Options" expanded="false"> 29 <section name="adv" title="Advanced Options" expanded="false">
29 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" /> 30 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" />
32 <param name="ratio" type="float" value="0.1" min="0.0" max="1.0" label="Ratio associated to each factor" /> 33 <param name="ratio" type="float" value="0.1" min="0.0" max="1.0" label="Ratio associated to each factor" />
33 </repeat> 34 </repeat>
34 </section> 35 </section>
35 </inputs> 36 </inputs>
36 <outputs> 37 <outputs>
37 <data name="sampling" format="tabular"> 38 <data name="output_sampling" format="tabular" label="${tool.name}" />
38 <discover_datasets pattern="__designation__" ext="tabular"/>
39 </data>
40 </outputs> 39 </outputs>
41 <tests> 40 <tests>
42 <!-- test 1: check if identical outputs are produced with default parameters --> 41 <!-- test 1: check if identical outputs are produced with default parameters -->
43 <test> 42 <test>
44 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> 43 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
45 <output name="sampling" ftype="tabular"> 44 <output name="sampling" file="sampler_sampling.test-1.tsv" ftype="tabular" compare="diff" />
46 <discovered_dataset designation="sampling.tsv" ftype="tabular">
47 <assert_contents>
48 <has_n_lines n="100"/>
49 <has_line_matching expression="^Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS$"/>
50 </assert_contents>
51 </discovered_dataset>
52 </output>
53 </test> 45 </test>
54 <!-- test 2: advanced arguments --> 46 <!-- test 2: advanced arguments -->
55 <test> 47 <test>
56 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> 48 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
57 <param name="nb_sampling_steps" value="3" /> 49 <param name="nb_sampling_steps" value="3" />
64 </repeat> 56 </repeat>
65 <repeat name="rep"> 57 <repeat name="rep">
66 <param name="ratio" value="0.3" /> 58 <param name="ratio" value="0.3" />
67 </repeat> 59 </repeat>
68 <param name="nb_samples" value="100" /> 60 <param name="nb_samples" value="100" />
69 <output name="sampling" ftype="tabular"> 61 <output name="sampling" file="sampler_sampling.test-2.tsv" ftype="tabular" compare="diff" />
70 <discovered_dataset designation="sampling.tsv" ftype="tabular">
71 <assert_contents>
72 <has_n_lines n="101"/>
73 <has_line_matching expression="^Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS$"/>
74 </assert_contents>
75 </discovered_dataset>
76 </output>
77 </test> 62 </test>
78 </tests> 63 </tests>
79 <help><![CDATA[ 64 <help><![CDATA[
80 Sampler 65 Sampler
81 ======= 66 =======