Mercurial > repos > sybila > ebcsgen_simulation

annotate ebcsgen_simulate.xml @ 2:bd726f013bc1 draft default tip

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 4719a69f514aed27d90c7017f052463b0b43cbb0
author sybila
date Sat, 15 Oct 2022 09:22:31 +0000
parents 179d32e79968
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179d32e79968 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
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1 <tool id="eBCSgen_simulate" name="eBCSgen simulation" version="@TOOL_VERSION@_galaxy0">
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2 <description>- simulate given model</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="creator"/>
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7 <requirements>
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8 <container type="docker">sybila/ebcsgen:v@TOOL_VERSION@</container>
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9 </requirements>
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10
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11 <command>python3 ${__tool_directory__}/ebcsgen_simulate.py
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12 --model '$model'
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13 --output '$output'
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14 --deterministic '$type.deterministic_choice'
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15 #if $type.deterministic_choice == "True":
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16 --direct False
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17 --runs 1
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18 --volume '$type.volume'
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19 --step '$type.step'
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20 #else:
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21 --direct '$type.network_free_choice'
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22 --runs '$type.num_of_runs'
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23 --volume 1
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24 --step 0.01
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25 #end if
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26 --max_time '$max_time'
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27 </command>
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28
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29 <inputs>
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30 <param format="bcsl.model" name="model" type="data" label="Model file" help="Provide a BCSL model file"/>
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31 <conditional name="type">
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32 <param name="deterministic_choice" type="select" label="Choose simulation method:">
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33 <option value="False" selected="true">Stochastic</option>
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34 <option value="True">Deterministic</option>
179d32e79968 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
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35 </param>
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36 <when value="False">
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37 <param name="network_free_choice" type="select" label="Choose network-free approach:">
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38 <option value="False" selected="true">Indirect</option>
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39 <option value="True">Direct</option>
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40 </param>
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41 <param name="num_of_runs" min="1" type="integer" value="1" label="Number of runs:"/>
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42 </when>
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43 <when value="True">
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44 <param name="volume" min="0" type="integer" value="1" label="Volume (liters):"/>
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45 <param name="step" min="0" type="float" value="0.01" label="Simulation step:"/>
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46 </when>
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47 </conditional>
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48 <param name="max_time" min="0" type="integer" value="1" label="Maximum simulation time:"/>
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49 </inputs>
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50
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51 <outputs>
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52 <data format="csv" name="output"/>
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
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58 <section name="type">
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59 <param name="deterministic_choice" value="True"/>
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60 <param name="step" value="0.1"/>
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61 </section>
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62 <param name="max_time" value="100"/>
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63 <output name="output" value="simulation_determ.csv" ftype="csv"/>
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64 </test>
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65 <test>
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66 <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
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67 <section name="type">
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68 <param name="deterministic_choice" value="False"/>
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69 <param name="network_free_choice" value="False"/>
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70 <param name="num_of_runs" value="2"/>
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71 </section>
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72 <param name="max_time" value="200"/>
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73 <output name="output" ftype="csv">
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74 <assert_contents>
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75 <has_n_columns n="4" sep=","/>
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76 <has_n_lines min="10"/>
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77 </assert_contents>
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78 </output>
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79 </test>
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80 <test>
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81 <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
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82 <section name="type">
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83 <param name="deterministic_choice" value="False"/>
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84 <param name="network_free_choice" value="True"/>
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85 <param name="num_of_runs" value="1"/>
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86 </section>
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87 <param name="max_time" value="100"/>
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88 <output name="output" ftype="csv">
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89 <assert_contents>
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90 <has_n_columns n="4" sep=","/>
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91 <has_n_lines min="10"/>
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92 </assert_contents>
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93 </output>
179d32e79968 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
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94 </test>
179d32e79968 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
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parents:
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95 </tests>
179d32e79968 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
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parents:
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96 </tool>