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comparison sampler.xml @ 2:d919d5c6f458 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 85162aa9b21ff6b297c164f127ed2ca2be2d90dd
author tduigou
date Wed, 08 Mar 2023 09:56:22 +0000
parents 80f5b5db4bb0
children fe4c1eccb687
comparison
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1:80f5b5db4bb0 2:d919d5c6f458
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 #set ratios = []
10 #for $x in $adv.rep 10 #for $x in $adv.rep
11 #silent ratios.append($x.ratio) 11 #silent $ratios.append(str($x.ratio))
12 #end for 12 #end for
13 #set sratios = ' '.join($ratios) 13 #set sratios = ' '.join(['"' + $x + '"' for $x in $ratios])
14 echo "${sratios}" &&
14 python -m icfree.sampler 15 python -m icfree.sampler
15 '$cfps_file' 16 '$cfps_file'
16 #if len(ratios) > 0 17 #if len(ratios) > 0
17 --sampling-ratios "${sratios}" 18 --sampling-ratios ${sratios}
18 #end if 19 #end if
19 --nb-sampling-steps '$adv.nb_sampling_steps' 20 --nb-sampling-steps '$adv.nb_sampling_steps'
20 --nb-samples '$adv.nb_samples' 21 --nb-samples '$adv.nb_samples'
21 --seed '0' 22 --seed '0'
22 --output-format 'tsv' 23 --output-format 'tsv'
23 --output-folder . && ls 24 --output-folder .
24 ]]></command> 25 ]]></command>
25 <inputs> 26 <inputs>
26 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" /> 27 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" />
27 <section name="adv" title="Advanced Options" expanded="false"> 28 <section name="adv" title="Advanced Options" expanded="false">
28 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" /> 29 <param name="nb_sampling_steps" type="integer" value="5" min="1" max="10" label="Number of values for all factors when performing the sampling" />
43 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" /> 44 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
44 <output name="sampling" ftype="tabular"> 45 <output name="sampling" ftype="tabular">
45 <discovered_dataset designation="sampling.tsv" ftype="tabular"> 46 <discovered_dataset designation="sampling.tsv" ftype="tabular">
46 <assert_contents> 47 <assert_contents>
47 <has_n_lines n="100"/> 48 <has_n_lines n="100"/>
49 <has_line_matching expression="^Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS$"/>
50 </assert_contents>
51 </discovered_dataset>
52 </output>
53 </test>
54 <!-- test 2: advanced arguments -->
55 <test>
56 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
57 <param name="nb_sampling_steps" value="3" />
58 <param name="nb_samples" value="100" />
59 <repeat name="rep">
60 <param name="ratio" value="0.4" />
61 </repeat>
62 <repeat name="rep">
63 <param name="ratio" value="0.2" />
64 </repeat>
65 <repeat name="rep">
66 <param name="ratio" value="0.3" />
67 </repeat>
68 <param name="nb_samples" value="100" />
69 <output name="sampling" ftype="tabular">
70 <discovered_dataset designation="sampling.tsv" ftype="tabular">
71 <assert_contents>
72 <has_n_lines n="101"/>
48 <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$"/> 73 <has_line_matching expression="^Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS$"/>
49 </assert_contents> 74 </assert_contents>
50 </discovered_dataset> 75 </discovered_dataset>
51 </output> 76 </output>
52 </test> 77 </test>