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changeset 8:eff04f7eec9f draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/55000e9b7d93cb8c8c45458c2bc152a47a6092a8 commit 55000e9b7d93cb8c8c45458c2bc152a47a6092a8-dirty"
author siwaa
date Mon, 26 Sep 2022 15:54:42 +0000
parents 39eb9b8f63e6
children b75e5e1a0646
files findidpairs.xml runsim.xml test-data/outputs/id-idSucc-pairs.csv
diffstat 3 files changed, 81 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/findidpairs.xml	Mon Sep 26 15:54:42 2022 +0000
@@ -0,0 +1,45 @@
+<tool id="CarboSeqFindIdPairs" name="CarboSeqFindIdPairs" version="1.0.0">
+  <description>To get IdPairs</description>
+  <requirements>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.1.0</container>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+  bash -e -c "mkdir inputs &&
+  cp ${meteo_data} inputs/meteo.csv &&
+  cp ${crop_data} inputs/crop.csv &&
+  cp ${soil_data} inputs/soil.csv &&
+  mkdir output &&
+  export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
+  export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) &&
+  Rscript /usr/local/src/myscripts/usercases/find-idPairs/run.r &&
+  cp output/id-idSucc-pairs.csv ${findpairs_output}"
+    ]]>
+  </command>
+  <inputs>
+    <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/>
+    <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/>
+    <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/>
+  </inputs>
+<outputs>
+  <data format='csv' name="findpairs_output" label="IdPairs"/>
+</outputs>
+<tests>
+  <test>
+    <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" />
+    <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" />
+    <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" />
+    <output name="findpairs_output" file="outputs/id-idSucc-pairs.csv" />
+  </test>
+</tests>
+<help>
+the CarboSeq find-idpairs tool
+==============================
+
+credits
+-------
+
+-  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
+-  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
+-  Copyright: INRAE
+</help>
+</tool>
--- a/runsim.xml	Mon Sep 05 07:54:50 2022 +0000
+++ b/runsim.xml	Mon Sep 26 15:54:42 2022 +0000
@@ -1,40 +1,44 @@
-<tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.0.0">
+<tool id="CarboSeqRunSim" name="CarboSeqRunSim" version="1.1.0">
   <description>To run the simulator</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.0.0</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:1.1.0</container>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-  bash -e -c "mkdir -p data/client.files &&
-  cp ${meteo_data} data/client.files/meteo.csv &&
-  cp ${crop_data} data/client.files/crop.csv &&
-  cp ${soil_data} data/client.files/soil.csv &&
-  mkdir -p data/mapping.files &&
-  cp ${crop_mapping} data/mapping.files/crop.mapping.csv &&
-  cp ${property_mapping} data/mapping.files/property.mapping.csv &&
+  bash -e -c "mkdir inputs &&
+  cp ${meteo_data} inputs/meteo.csv &&
+  cp ${crop_data} inputs/crop.csv &&
+  cp ${soil_data} inputs/soil.csv &&
   mkdir output &&
   export CSOPRALIBS_PARAM_OUTPUT=\$(realpath -s output) &&
-  cp /usr/local/src/myscripts/usercases/run-sim/run.r . &&
-  Rscript run.r &&
+  export CSVMAPPER_INPUT_DIR=\$(realpath -s inputs) &&
+  #if $id_pairs
+  export CSOPRALIBS_ID_IDSUCC_CSV_FILE=${id_pairs} &&
+  #end if
+  export CSOPRALIBS_SIM_PARAMS_IMPLEMENTATION=${simulator} &&
+  Rscript /usr/local/src/myscripts/usercases/run-sim/run.r &&
   cp output/SimulationSOCResults.RData ${run_output}"
     ]]>
   </command>
   <inputs>
-    <param name="meteo_data" type="data" format="csv" label="meteo data (csv file)"/>
-    <param name="crop_data" type="data" format="csv" label="crop data (csv file)"/>
-    <param name="soil_data" type="data" format="csv" label="soil data (csv file)"/>
-    <param name="crop_mapping" type="data" format="csv" label="crop mapping (csv file)"/>
-    <param name="property_mapping" type="data" format="csv" label="property mapping (csv file)"/>
+    <param name="simulator" type="select" label="Simulator">
+      <option value="rothC" selected="true">rothC</option>
+      <option value="soilr">soilr</option>
+    </param>
+    <param name="meteo_data" type="data" format="csv" label="Meteo data (csv file)"/>
+    <param name="crop_data" type="data" format="csv" label="Crop data (csv file)"/>
+    <param name="soil_data" type="data" format="csv" label="Soil data (csv file)"/>
+    <param name="id_pairs" type="data" optional="true" format="csv" label="Id pairs (csv file)"/>
   </inputs>
 <outputs>
   <data format='rdata' name="run_output" label="Simulation SOC Results"/>
 </outputs>
 <tests>
-  <test>
+  <test>    
+    <param name="simulator" value="rothC" />
+    <param name="id_pairs" value="outputs/id-idSucc-pairs.csv" ftype="csv"/>
     <param name="meteo_data" value="inputs/client.files/meteo.csv" ftype="csv" />
     <param name="crop_data" value="inputs/client.files/crop.csv" ftype="csv" />
     <param name="soil_data" value="inputs/client.files/soil.csv" ftype="csv" />
-    <param name="crop_mapping" value="inputs/mapping.files/crop.mapping.csv" ftype="csv" />
-    <param name="property_mapping" value="inputs/mapping.files/property.mapping.csv" ftype="csv"/>
     <output name="run_output">
     <assert_contents>
       <has_size value="5462" delta="100" />
@@ -43,14 +47,13 @@
   </test>
 </tests>
 <help>
-the CarboSeqPrepareSim tool
-===========================
+the CarboSeq run-sim  tool
+==========================
 
 credits
 -------
 
 -  Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
--  Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
 -  Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
 -  Copyright: INRAE
 </help>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outputs/id-idSucc-pairs.csv	Mon Sep 26 15:54:42 2022 +0000
@@ -0,0 +1,11 @@
+"id_profil_csopra","id_succession"
+1,1
+2,1
+3,1
+4,1
+5,1
+6,1
+7,1
+8,1
+9,1
+10,1