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changeset 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
files default/cow_parameters.json default/goat_parameters.json tools_grum.xml
diffstat 3 files changed, 30 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/default/cow_parameters.json	Tue Aug 24 13:04:11 2021 +0000
+++ b/default/cow_parameters.json	Fri Jan 21 08:35:16 2022 +0000
@@ -8,5 +8,5 @@
     "kmd": { "low": 0.0001, "high": 0.01},
     "kmr_glob": [0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01],
     "gam_glob": [0.0000035, 281],
-    "kg_glob": 0.002
+    "kg": { "low": 0.001, "high": 0.003}
 }
--- a/default/goat_parameters.json	Tue Aug 24 13:04:11 2021 +0000
+++ b/default/goat_parameters.json	Fri Jan 21 08:35:16 2022 +0000
@@ -8,5 +8,5 @@
     "kmd": { "low": 0.002, "high": 0.02},
     "kmr_glob": [0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.02],
     "gam_glob": [0.0005, 150.0],
-    "kg_glob": 0.002
+    "kg": { "low": 0.001, "high": 0.003}
 }
--- a/tools_grum.xml	Tue Aug 24 13:04:11 2021 +0000
+++ b/tools_grum.xml	Fri Jan 21 08:35:16 2022 +0000
@@ -1,7 +1,7 @@
-<tool id="GRUM" name="GRUM, Estimate the values of parameters" version="1.2.0">
-  <description></description>
+<tool id="GRUM" name="GRUM parameters estimation" version="1.3.0">
+  <description>Estimate the values of parameters of the GRUM lifetime weight trajectories in livestock female model</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/grum/grum:1.2</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/grum/grum:1.3</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[
@@ -13,23 +13,31 @@
 	        #end if
 	     #elif str( $selectAction.action ) == 'estimateParameters':
                 #if str( $selectAction.mammalParamSet.choose ) == 'defaultGoat':
-	           /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';";
+                   cp '$__tool_directory__/default/goat_parameters.json' mammal_parameters.json;
 		   #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
                       cp '$__tool_directory__/default/goat_parameters.json' ${parameter_values_file};
 		   #end if   
 	           #elif str( $selectAction.mammalParamSet.choose ) == 'defaultCow':
-                   /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';";
+                   cp '$__tool_directory__/default/cow_parameters.json' mammal_parameters.json;
 		   #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
                       cp '$__tool_directory__/default/cow_parameters.json' ${parameter_values_file};
 		   #end if   
 	           #elif str( $selectAction.mammalParamSet.choose ) == 'customMammal':
-                   /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} ;";
+                   cp ${selectAction.mammalParamSet.parameterValues_input} mammal_parameters.json;
 		   #if str( $selectAction.do_output_parameterValues ) == 'do_output_parameterValues':
                      cp ${selectAction.mammalParamSet.parameterValues_input} ${parameter_values_file};
 	           #end if
 	        #end if
+		head -n 1  ${selectAction.litter_input} > litter.csv;
+		head -n 1  ${selectAction.bw_input} > bw.csv;
+		#for $id in $selectAction.ids
+		   grep $id ${selectAction.litter_input} >> litter.csv;
+		   grep $id ${selectAction.bw_input} >> bw.csv;
+		#end for
+	        /bin/bash -c "Rscript --verbose /data/grum/siwaa_recipe/grum_siwaa.R litter.csv bw.csv ${selectAction.do_plot_fitted} mammal_parameters.json";
+
 		#if str( $selectAction.do_plot_fitted ) == 'do_plot_fitted':
-                   pdfunite goat_*.pdf simulation_plots.pdf;
+                   pdfunite mammal_*.pdf simulation_plots.pdf;
                    cp simulation_plots.pdf ${simulation_plots};
                 #end if
 	     cp estimated_parameters.csv ${estimated_parameters};
@@ -39,12 +47,20 @@
   <inputs>
     <conditional name="selectAction">
       <param name="action" type="select" label="Select the action to perform">
-	<option value="estimateParameters" selected="true">estimate Goat parameters values</option>
-	<option value="getDefaultInitial">get default Goat initial parameters initial values</option>
+	<option value="estimateParameters" selected="true">estimate mammal parameters values</option>
+	<option value="getDefaultInitial">get default mammal initial parameters initial values</option>
       </param>
       <when value="estimateParameters">
-	<param name="litter_input" type="data" format="csv" label="Litter file" optional="true"/>
-	<param name="bw_input" type="data" format="csv" label="Body weight file" optional="true"/>
+	<param name="litter_input" type="data" format="csv" label="Litter file" optional="false"/>
+	<param name="bw_input" type="data" format="csv" label="Body weight file" optional="false"/>
+	<param name="ids" type="select" checked="true" optional="false" multiple="true" label="Select a set of mammals">
+	  <options from_dataset="litter_input"  separator=";">
+            <column name="name" index="0"/>
+            <column name="value" index="0"/>
+	    <filter type="unique_value" name="unique_param" column="0"/>
+	    <filter type="remove_value" value='"id"' />
+	  </options>
+    </param>
 	<conditional name="mammalParamSet">
 	  <param name="choose" type="select" label="Select the mammal parameters initial values">
 	    <option value="defaultGoat" selected="true">default Goat parameters initiale values</option>
@@ -99,6 +115,7 @@
       </conditional>
       <param name="litter_input" value="inputs/Litter_test.csv" ftype="csv" />
       <param name="bw_input" value="inputs/BW_test.csv" ftype="csv" />
+      <param name="ids" value="2004029,2005115" />
       <conditional name="mammalParam">
 	<param name="choose" value="defaultGoat"/>
       </conditional>