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annotate tools_grum.xml @ 2:21c154989717 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit b956f127cf3e2e20dda2bb2b93ce8925eea589ef"
author siwaa
date Wed, 10 Aug 2022 12:30:47 +0000
parents 9c1c1c7f0e48
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9c1c1c7f0e48 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 83cff75a84aef58a825abe715aced1922456b088"
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1 <tool id="GRUM" name="GRUM parameters estimation" version="1.3.0">
9c1c1c7f0e48 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 83cff75a84aef58a825abe715aced1922456b088"
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2 <description>Estimate the values of parameters of the GRUM lifetime weight trajectories in livestock female model</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/grum/grum:1.3</container>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
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8 #if str( $selectAction.action ) == 'getDefaultInitial':
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9 #if str( $selectAction.mammalParamGet.choose ) == 'defaultGoat':
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10 cp '$__tool_directory__/default/goat_parameters.json' ${parameter_values_file_only};
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11 #elif str( $selectAction.mammalParamGet.choose ) == 'defaultCow':
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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12 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file_only};
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13 #end if
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14 #elif str( $selectAction.action ) == 'estimateParameters':
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15 #if str( $selectAction.mammalParamSet.choose ) == 'defaultGoat':
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16 cp '$__tool_directory__/default/goat_parameters.json' mammal_parameters.json;
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17 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
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18 cp '$__tool_directory__/default/goat_parameters.json' ${parameter_values_file};
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19 #end if
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20 #elif str( $selectAction.mammalParamSet.choose ) == 'defaultCow':
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21 cp '$__tool_directory__/default/cow_parameters.json' mammal_parameters.json;
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22 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
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23 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file};
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24 #end if
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25 #elif str( $selectAction.mammalParamSet.choose ) == 'customMammal':
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26 cp ${selectAction.mammalParamSet.parameterValues_input} mammal_parameters.json;
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27 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
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28 cp ${selectAction.mammalParamSet.parameterValues_input} ${parameter_values_file};
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29 #end if
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30 #end if
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31 head -n 1 ${selectAction.litter_input} > litter.csv;
9c1c1c7f0e48 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 83cff75a84aef58a825abe715aced1922456b088"
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32 head -n 1 ${selectAction.bw_input} > bw.csv;
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33 #for $id in $selectAction.ids
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34 grep $id ${selectAction.litter_input} >> litter.csv;
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35 grep $id ${selectAction.bw_input} >> bw.csv;
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36 #end for
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37 /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R litter.csv bw.csv ${selectAction.do_plot_fitted} mammal_parameters.json";
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38
0
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39 #if str( $selectAction.do_plot_fitted ) == 'do_plot_fitted':
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40 pdfunite mammal_*.pdf simulation_plots.pdf;
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41 cp simulation_plots.pdf ${simulation_plots};
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42 #end if
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43 cp estimated_parameters.csv ${estimated_parameters};
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44 #end if
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45 ]]>
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46 </command>
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47 <inputs>
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48 <conditional name="selectAction">
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49 <param name="action" type="select" label="Select the action to perform">
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50 <option value="estimateParameters" selected="true">estimate mammal parameters values</option>
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51 <option value="getDefaultInitial">get default mammal initial parameters initial values</option>
0
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52 </param>
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53 <when value="estimateParameters">
1
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54 <param name="litter_input" type="data" format="csv" label="Litter file" optional="false"/>
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55 <param name="bw_input" type="data" format="csv" label="Body weight file" optional="false"/>
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56 <param name="ids" type="select" checked="true" optional="false" multiple="true" label="Select a set of mammals">
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57 <options from_dataset="litter_input" separator=",">
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58 <column name="name" index="0"/>
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59 <column name="value" index="0"/>
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60 <filter type="unique_value" name="unique_param" column="0"/>
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61 <filter type="remove_value" value='"id"' />
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62 </options>
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63 </param>
0
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64 <conditional name="mammalParamSet">
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65 <param name="choose" type="select" label="Select the mammal parameters initial values">
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66 <option value="defaultGoat" selected="true">default Goat parameters initiale values</option>
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67 <option value="defaultCow">default Cow parameters initial values</option>
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68 <option value="customMammal">custom Mammal parameters initial values</option>
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69 </param>
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70 <when value="customMammal">
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71 <param name="parameterValues_input" type="data" format="json" label="Select a mammal parameters initial values file(json)"/>
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72 </when>
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73 <when value="defaultGoat">
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74 </when>
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75 <when value="defaultCow">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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76 </when>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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77 </conditional>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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78 <param name="do_plot_fitted" type="boolean" checked="true" label="Plot fitted"
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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79 truevalue="do_plot_fitted" falsevalue="do_not_plot_fitted" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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80 <param name="do_output_parameterValues" type="boolean" checked="true" label="Output the parameter Values file"
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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81 truevalue="do_output_parameterValues" falsevalue="do_not_outputParametersValues" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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82 </when>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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83 <when value="getDefaultInitial">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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84 <conditional name="mammalParamGet">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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85 <param name="choose" type="select" label="Select the mammal parameter values">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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86 <option value="defaultGoat" selected="true">default Goat parameters initial values</option>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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87 <option value="defaultCow">default Cow parameters initial values</option>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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88 </param>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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89 <when value="defaultGoat">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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90 </when>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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91 <when value="defaultCow">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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92 </when>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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93 </conditional>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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94 </when>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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95 </conditional>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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96 </inputs>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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97 <outputs>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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98 <data format="csv" name="estimated_parameters" label="GRUM estimated parameters" >
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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99 <filter>selectAction['action'] == 'estimateParameters'</filter>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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100 </data>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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101 <data format="pdf" name="simulation_plots" label="GRUM plots" >
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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102 <filter>selectAction['action'] == 'estimateParameters' and selectAction['do_plot_fitted']</filter>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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103 </data>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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104 <data format="json" name="parameter_values_file_only" label="Parameters initial values" >
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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105 <filter>selectAction['action'] == 'getDefaultInitial'</filter>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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106 </data>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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107 <data format="json" name="parameter_values_file" label="Parameters initial values" >
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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108 <filter>selectAction['action'] == 'estimateParameters' and selectAction['do_output_parameterValues']</filter>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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109 </data>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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110 </outputs>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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111 <tests>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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112 <test>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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113 <conditional name="selectAction">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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114 <param name="action" value="estimateParameters"/>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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115 </conditional>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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116 <param name="litter_input" value="inputs/Litter_test.csv" ftype="csv" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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117 <param name="bw_input" value="inputs/BW_test.csv" ftype="csv" />
2
21c154989717 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit b956f127cf3e2e20dda2bb2b93ce8925eea589ef"
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118 <param name="ids" value='"2004029","2005115"' />
0
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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119 <conditional name="mammalParam">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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120 <param name="choose" value="defaultGoat"/>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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121 </conditional>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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122 <param name="do_plot_fitted" value="true" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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123 <output name="estimated_parameters" ftype="csv">
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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124 <assert_contents>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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125 <has_line line="&quot;ID&quot;,&quot;W0&quot;,&quot;G0&quot;,&quot;kr_1&quot;,&quot;kUa_1&quot;,&quot;kUf_1&quot;,&quot;kn_1&quot;,&quot;kmd_1&quot;,&quot;kr_2&quot;,&quot;kUa_2&quot;,&quot;kUf_2&quot;,&quot;kn_2&quot;,&quot;kmd_2&quot;" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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126 <has_line_matching expression="&quot;X2004029&quot;,.*" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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127 <has_line_matching expression="&quot;X2005115&quot;,.*" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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128 <has_n_columns n="13" sep=","/>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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129 <has_n_lines n="3" />
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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130 </assert_contents>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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131 </output>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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132 </test>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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133 </tests>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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134 <help>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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135 Inputs:
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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136 =======
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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137
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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138 - Litter for each mammal.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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139 - Sequence of body weight of mammals.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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140 - (optional) Initial parameter values for the estimation process, if the defaults available are not revelant.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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141
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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142 Outputs:
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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143 ========
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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144
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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145 - Estimated parameters for each goat (csv file).
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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146 - (optional) Plots of simulations with estimated parameters for each goat (pdf file).
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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147 - (optional) Initial parameters values used for the estimation process (json file)
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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148
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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149 Example:
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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150 ========
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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151
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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152 - Copy to your history files BW_smalltable.csv and Litter_smalltable.csv from GRUM Datasets.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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153 - Select default initial parameter values set, or provide one.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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154 - Fill filenames and choose the adequate number of cores.
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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155 - And then execute (it takes around 20 minutes per goat for estimation)
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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156
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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157 </help>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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158 </tool>
c65c94b47771 "planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 5dce511538bebef7453c594f68ea7d13e8fc3ea8"
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159