Mercurial > repos > tduigou > icfree_sampler

annotate 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
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a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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1 <tool id="icfree_sampler" name="iCFree sampler" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Generate data points using latin hypercube sampling (LHS)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #set ratios = []
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10 #for $x in $adv.rep
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11 #silent $ratios.append(str($x.ratio))
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12 #end for
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13 #set sratios = ' '.join(['"' + $x + '"' for $x in $ratios])
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14 echo "${sratios}" &&
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15 python -m icfree.sampler
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16 '$cfps_file'
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17 #if len(ratios) > 0
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18 --sampling-ratios ${sratios}
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19 #end if
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20 --nb-sampling-steps '$adv.nb_sampling_steps'
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21 --nb-samples '$adv.nb_samples'
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22 --seed '0'
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23 --output-format 'tsv'
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24 --output-folder .
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25 ]]></command>
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26 <inputs>
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27 <param name="cfps_file" type="data" format="tabular" label="CFPS parameters and features" />
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28 <section name="adv" title="Advanced Options" expanded="false">
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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" />
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30 <param name="nb_samples" type="integer" value="99" min="1" max="198" label="Number of samples to generate" />
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31 <repeat name="rep" title="Sampling ratio" min="0">
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32 <param name="ratio" type="float" value="0.1" min="0.0" max="1.0" label="Ratio associated to each factor" />
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33 </repeat>
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34 </section>
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35 </inputs>
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36 <outputs>
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37 <data name="sampling" format="tabular">
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38 <discover_datasets pattern="__designation__" ext="tabular"/>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <!-- test 1: check if identical outputs are produced with default parameters -->
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43 <test>
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44 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
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45 <output name="sampling" ftype="tabular">
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46 <discovered_dataset designation="sampling.tsv" ftype="tabular">
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47 <assert_contents>
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48 <has_n_lines n="100"/>
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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$"/>
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50 </assert_contents>
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51 </discovered_dataset>
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52 </output>
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53 </test>
2
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54 <!-- test 2: advanced arguments -->
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55 <test>
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56 <param name="cfps_file" value="converter_proCFPS_parameters.tsv" />
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57 <param name="nb_sampling_steps" value="3" />
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58 <param name="nb_samples" value="100" />
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59 <repeat name="rep">
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60 <param name="ratio" value="0.4" />
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61 </repeat>
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62 <repeat name="rep">
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63 <param name="ratio" value="0.2" />
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64 </repeat>
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65 <repeat name="rep">
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66 <param name="ratio" value="0.3" />
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67 </repeat>
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68 <param name="nb_samples" value="100" />
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69 <output name="sampling" ftype="tabular">
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70 <discovered_dataset designation="sampling.tsv" ftype="tabular">
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71 <assert_contents>
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72 <has_n_lines n="101"/>
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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$"/>
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74 </assert_contents>
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75 </discovered_dataset>
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76 </output>
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77 </test>
0
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78 </tests>
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79 <help><![CDATA[
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80 Sampler
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81 =======
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82
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83 This module generates a list of values for all parameters given in the input file.
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84 The values are generated using a Latin Hypercube Sampling (LHS) method (lhs function from the pyDOE package).
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85 The number of values generated is given by the user and the values are saved in csv or tsv file.
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86
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87 It is important to note that the user can pass some values that he whishes to combine. In this case, we are dealing with discrete space, and because LHS is working on continuous space the result sampling can contain duplicates.
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88 To avoid this, we have set some filters to select the appropriate sampling method:
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89
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90 * If the result sampling contain duplicates, then we replace them by random samples.
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91 * Proceed with full random sampling.
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92 * Generate all the combinations.
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93
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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94 Input
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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95 -----
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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96 * **CFPS Parameters File**: The first column is the parameter (or factor) names. The second column is the maxValue of the parameter that will be used in the sampling. The third column is the concnetration of the stock. The fourth column is the deadVolume of the parameter. This is used to calculate the volume of the parameter that will not be pipetted by the robot (because of viscosity). The fifth column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options. If one single number is given, then take this number as a const value.
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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97
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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98 Advanced options:
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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99 -----------------
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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100 * **Number of sampling steps**: Number of values for all factors when performing the sampling (default: 5)
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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101 * **Sampling ratios**: Ratios for all factors when performing the sampling
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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102 * **Number of samples**: Number of samples to generate for all factors when performing the sampling (default: 99)
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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103
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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104 Output
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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105 ------
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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106 * a TSV file with the sampling values for each parameter
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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107 ]]></help>
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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108 <expand macro="creator"/>
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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109 <expand macro="citation"/>
a71884785dcc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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110 </tool>