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comparison sampler.xml @ 5:b2dba600eb2b draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 1568ac8d21ca92c2325ef661498ee7a4b622ae5e
author tduigou
date Tue, 21 Mar 2023 09:43:44 +0000
parents fe4c1eccb687
children 40b05ca455a9
comparison
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4:fe4c1eccb687 5:b2dba600eb2b
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #set ratios = [] 9 echo '$adv.sampling_ratio' &&
10 #for $x in $adv.rep
11 #silent $ratios.append(str($x.ratio))
12 #end for
13 #set sratios = ' '.join(['"' + $x + '"' for $x in $ratios])
14 echo "${sratios}" &&
15 python -m icfree.sampler 10 python -m icfree.sampler
16 '$cfps_file' 11 '$cfps_file'
17 #if len(ratios) > 0 12 --nb-sampling-steps '$adv.nb_sampling_steps'
18 --sampling-ratios ${sratios} 13 --nb-samples '$nb_samples'
14 #if str($adv.sampling_ratio) != ""
15 #set ratios = ' '.join(['"' + $x + '"' for $x in $adv.sampling_ratio.split()])
16 --sampling-ratios $ratios
19 #end if 17 #end if
20 --nb-sampling-steps '$adv.nb_sampling_steps' 18 #if str($adv.seed_cond.seed_param) == 'not_random'
21 --nb-samples '$adv.nb_samples' 19 --seed '$adv.seed_cond.seed'
22 --seed '0' 20 #end if
23 --output-format 'tsv' 21 --output-format 'tsv'
24 --output-folder . && 22 --output-folder . &&
25 mv sampling.tsv '$output_sampling' 23 mv sampling.tsv '$output_sampling'
26 ]]></command> 24 ]]></command>
27 <inputs> 25 <inputs>
28 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" /> 26 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" />
27 <param name="nb_samples" type="integer" value="99" min="1" max="198" label="Number of samples to generate" />
29 <section name="adv" title="Advanced Options" expanded="false"> 28 <section name="adv" title="Advanced Options" expanded="false">
30 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" /> 29 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" />
31 <param name="nb_samples" type="integer" value="99" min="1" max="198" label="Number of samples to generate" /> 30 <param name="sampling_ratio" type="text" value="" label="Ratios associated for all factors" help="Only float, space separated, are allowed">
32 <repeat name="rep" title="Sampling ratio" min="0"> 31 <validator type="regex" message="Float separated by a space between in the range: 0.0 - 1.0">^(?:(0.\d+|1\.0)(\s0?\.\d+|1\.0)*)*$</validator>
33 <param name="ratio" type="float" value="0.1" min="0.0" max="1.0" label="Ratio associated to each factor" /> 32 </param>
34 </repeat> 33 <conditional name="seed_cond">
34 <param name="seed_param" type="select" label="Seed" help="Choose a seed or let it as random">
35 <option value="random" selected="true">random</option>
36 <option value="not_random">fixed</option>
37 </param>
38 <when value="random"/>
39 <when value="not_random">
40 <param name="seed" type="text" value="0" label="Seed value" help="Only integer allowed">
41 <validator type="empty_field" message="Not empty, select random"/>
42 <validator type="regex" message="Only integer allowed">^(?:\d+)$</validator>
43 </param>
44 </when>
45 </conditional>
35 </section> 46 </section>
36 </inputs> 47 </inputs>
37 <outputs> 48 <outputs>
38 <data name="output_sampling" format="tabular" label="${tool.name}" /> 49 <data name="output_sampling" format="tabular" label="${tool.name}" />
39 </outputs> 50 </outputs>
40 <tests> 51 <tests>
41 <!-- test 1: check if identical outputs are produced with default parameters --> 52 <!-- test 1: check if identical outputs are produced with default parameters -->
42 <test> 53 <test>
43 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> 54 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
55 <param name="seed_param" value="not_random" />
56 <param name="seed" value="0" />
44 <output name="sampling" file="sampler_sampling.test-1.tsv" ftype="tabular" compare="diff" /> 57 <output name="sampling" file="sampler_sampling.test-1.tsv" ftype="tabular" compare="diff" />
45 </test> 58 </test>
46 <!-- test 2: advanced arguments --> 59 <!-- test 2: advanced arguments -->
47 <test> 60 <test>
48 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> 61 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
49 <param name="nb_sampling_steps" value="3" /> 62 <param name="nb_sampling_steps" value="3" />
50 <param name="nb_samples" value="100" /> 63 <param name="nb_samples" value="100" />
51 <repeat name="rep"> 64 <param name="sampling_ratio" value="0.4 0.2 0.3" />
52 <param name="ratio" value="0.4" /> 65 <param name="seed_param" value="not_random" />
53 </repeat> 66 <param name="seed" value="0" />
54 <repeat name="rep">
55 <param name="ratio" value="0.2" />
56 </repeat>
57 <repeat name="rep">
58 <param name="ratio" value="0.3" />
59 </repeat>
60 <param name="nb_samples" value="100" /> 67 <param name="nb_samples" value="100" />
61 <output name="sampling" file="sampler_sampling.test-2.tsv" ftype="tabular" compare="diff" /> 68 <output name="sampling" file="sampler_sampling.test-2.tsv" ftype="tabular" compare="diff" />
62 </test> 69 </test>
63 </tests> 70 </tests>
64 <help><![CDATA[ 71 <help><![CDATA[