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comparison tools_grum.xml @ 1:9c1c1c7f0e48 draft

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"planemo upload for repository https://forgemia.inra.fr/grum/grum/-/tree/master/siwaa_recipe/galaxy_tools commit 83cff75a84aef58a825abe715aced1922456b088"
author siwaa
date Fri, 21 Jan 2022 08:35:16 +0000
parents c65c94b47771
children 21c154989717
comparison
equal deleted inserted replaced
0:c65c94b47771 1:9c1c1c7f0e48
1 <tool id="GRUM" name="GRUM, Estimate the values of parameters" version="1.2.0"> 1 <tool id="GRUM" name="GRUM parameters estimation" version="1.3.0">
2 <description></description> 2 <description>Estimate the values of parameters of the GRUM lifetime weight trajectories in livestock female model</description>
3 <requirements> 3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/grum/grum:1.2</container> 4 <container type="singularity">docker://registry.forgemia.inra.fr/grum/grum:1.3</container>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 <![CDATA[ 7 <![CDATA[
8 #if str( $selectAction.action ) == 'getDefaultInitial': 8 #if str( $selectAction.action ) == 'getDefaultInitial':
9 #if str( $selectAction.mammalParamGet.choose ) == 'defaultGoat': 9 #if str( $selectAction.mammalParamGet.choose ) == 'defaultGoat':
11 #elif str( $selectAction.mammalParamGet.choose ) == 'defaultCow': 11 #elif str( $selectAction.mammalParamGet.choose ) == 'defaultCow':
12 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file_only}; 12 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file_only};
13 #end if 13 #end if
14 #elif str( $selectAction.action ) == 'estimateParameters': 14 #elif str( $selectAction.action ) == 'estimateParameters':
15 #if str( $selectAction.mammalParamSet.choose ) == 'defaultGoat': 15 #if str( $selectAction.mammalParamSet.choose ) == 'defaultGoat':
16 /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R ${selectAction.litter_input} ${selectAction.bw_input} ${selectAction.do_plot_fitted} '$__tool_directory__/default/goat_parameters.json';"; 16 cp '$__tool_directory__/default/goat_parameters.json' mammal_parameters.json;
17 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues': 17 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
18 cp '$__tool_directory__/default/goat_parameters.json' ${parameter_values_file}; 18 cp '$__tool_directory__/default/goat_parameters.json' ${parameter_values_file};
19 #end if 19 #end if
20 #elif str( $selectAction.mammalParamSet.choose ) == 'defaultCow': 20 #elif str( $selectAction.mammalParamSet.choose ) == 'defaultCow':
21 /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R ${selectAction.litter_input} ${selectAction.bw_input} ${selectAction.do_plot_fitted} '$__tool_directory__/default/cow_parameters.json';"; 21 cp '$__tool_directory__/default/cow_parameters.json' mammal_parameters.json;
22 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues': 22 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
23 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file}; 23 cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file};
24 #end if 24 #end if
25 #elif str( $selectAction.mammalParamSet.choose ) == 'customMammal': 25 #elif str( $selectAction.mammalParamSet.choose ) == 'customMammal':
26 /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R ${selectAction.litter_input} ${selectAction.bw_input} ${selectAction.do_plot_fitted} ${selectAction.mammalParamSet.parameterValues_input} ;"; 26 cp ${selectAction.mammalParamSet.parameterValues_input} mammal_parameters.json;
27 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues': 27 #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
28 cp ${selectAction.mammalParamSet.parameterValues_input} ${parameter_values_file}; 28 cp ${selectAction.mammalParamSet.parameterValues_input} ${parameter_values_file};
29 #end if 29 #end if
30 #end if 30 #end if
31 head -n 1 ${selectAction.litter_input} > litter.csv;
32 head -n 1 ${selectAction.bw_input} > bw.csv;
33 #for $id in $selectAction.ids
34 grep $id ${selectAction.litter_input} >> litter.csv;
35 grep $id ${selectAction.bw_input} >> bw.csv;
36 #end for
37 /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R litter.csv bw.csv ${selectAction.do_plot_fitted} mammal_parameters.json";
38
31 #if str( $selectAction.do_plot_fitted ) == 'do_plot_fitted': 39 #if str( $selectAction.do_plot_fitted ) == 'do_plot_fitted':
32 pdfunite goat_*.pdf simulation_plots.pdf; 40 pdfunite mammal_*.pdf simulation_plots.pdf;
33 cp simulation_plots.pdf ${simulation_plots}; 41 cp simulation_plots.pdf ${simulation_plots};
34 #end if 42 #end if
35 cp estimated_parameters.csv ${estimated_parameters}; 43 cp estimated_parameters.csv ${estimated_parameters};
36 #end if 44 #end if
37 ]]> 45 ]]>
38 </command> 46 </command>
39 <inputs> 47 <inputs>
40 <conditional name="selectAction"> 48 <conditional name="selectAction">
41 <param name="action" type="select" label="Select the action to perform"> 49 <param name="action" type="select" label="Select the action to perform">
42 <option value="estimateParameters" selected="true">estimate Goat parameters values</option> 50 <option value="estimateParameters" selected="true">estimate mammal parameters values</option>
43 <option value="getDefaultInitial">get default Goat initial parameters initial values</option> 51 <option value="getDefaultInitial">get default mammal initial parameters initial values</option>
44 </param> 52 </param>
45 <when value="estimateParameters"> 53 <when value="estimateParameters">
46 <param name="litter_input" type="data" format="csv" label="Litter file" optional="true"/> 54 <param name="litter_input" type="data" format="csv" label="Litter file" optional="false"/>
47 <param name="bw_input" type="data" format="csv" label="Body weight file" optional="true"/> 55 <param name="bw_input" type="data" format="csv" label="Body weight file" optional="false"/>
56 <param name="ids" type="select" checked="true" optional="false" multiple="true" label="Select a set of mammals">
57 <options from_dataset="litter_input" separator=";">
58 <column name="name" index="0"/>
59 <column name="value" index="0"/>
60 <filter type="unique_value" name="unique_param" column="0"/>
61 <filter type="remove_value" value='"id"' />
62 </options>
63 </param>
48 <conditional name="mammalParamSet"> 64 <conditional name="mammalParamSet">
49 <param name="choose" type="select" label="Select the mammal parameters initial values"> 65 <param name="choose" type="select" label="Select the mammal parameters initial values">
50 <option value="defaultGoat" selected="true">default Goat parameters initiale values</option> 66 <option value="defaultGoat" selected="true">default Goat parameters initiale values</option>
51 <option value="defaultCow">default Cow parameters initial values</option> 67 <option value="defaultCow">default Cow parameters initial values</option>
52 <option value="customMammal">custom Mammal parameters initial values</option> 68 <option value="customMammal">custom Mammal parameters initial values</option>
97 <conditional name="selectAction"> 113 <conditional name="selectAction">
98 <param name="action" value="estimateParameters"/> 114 <param name="action" value="estimateParameters"/>
99 </conditional> 115 </conditional>
100 <param name="litter_input" value="inputs/Litter_test.csv" ftype="csv" /> 116 <param name="litter_input" value="inputs/Litter_test.csv" ftype="csv" />
101 <param name="bw_input" value="inputs/BW_test.csv" ftype="csv" /> 117 <param name="bw_input" value="inputs/BW_test.csv" ftype="csv" />
118 <param name="ids" value="2004029,2005115" />
102 <conditional name="mammalParam"> 119 <conditional name="mammalParam">
103 <param name="choose" value="defaultGoat"/> 120 <param name="choose" value="defaultGoat"/>
104 </conditional> 121 </conditional>
105 <param name="do_plot_fitted" value="true" /> 122 <param name="do_plot_fitted" value="true" />
106 <output name="estimated_parameters" ftype="csv"> 123 <output name="estimated_parameters" ftype="csv">