Mercurial > repos > siwaa > azodyn

changeset 3:d1070fee9dc4 draft

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"planemo upload for repository https://forgemia.inra.fr/record/RECORD/-/tree/master/misc/galaxy_tools commit 4861ee70e49274ed88d2b7ca37f02178ed6da471"
author siwaa
date Wed, 27 Apr 2022 09:59:49 +0000
parents e6bbaf03133e
children 5deede146fb6
files tool_AZODYN.xml tool_AZODYN.xml.bak
diffstat 2 files changed, 10 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/tool_AZODYN.xml	Wed Nov 17 14:23:35 2021 +0000
+++ b/tool_AZODYN.xml	Wed Apr 27 09:59:49 2022 +0000
@@ -1,11 +1,14 @@
 <tool id="AZODYN" name="AZODYN crop models simulations" version="1.0.0">
   <description></description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:187cf18876225903f7ab06915374a0277ad83130</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container>
   </requirements>
   <command detect_errors="aggressive">
     unzip ${input_meteo}; 
-    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R ${crop_type} AZODYN ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
+    dos2unix -n ${file_input} internal_inputAZODYN.csv
+    dos2unix -n ${file_outputs} internal_outputAZODYN.csv
+ 
+    /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
     zip temp_results.zip  simresults_*.txt;
     cp temp_results.zip ${simresults};
   </command>
--- a/tool_AZODYN.xml.bak	Wed Nov 17 14:23:35 2021 +0000
+++ b/tool_AZODYN.xml.bak	Wed Apr 27 09:59:49 2022 +0000
@@ -1,11 +1,14 @@
 <tool id="AZODYN" name="AZODYN crop models simulations" version="1.0.0">
   <description></description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:latest</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/record/record/azodyn_sunflo:ub2004_vle21</container>
   </requirements>
   <command detect_errors="aggressive">
     unzip ${input_meteo}; 
-    /bin/bash -c "Rscript --verbose /data/RECORD/misc/docker/rAzodynSunflo.R ${crop_type} AZODYN ${file_input} ${file_outputs} \${GALAXY_SLOTS:-2}";
+    dos2unix -n ${file_input} internal_inputAZODYN.csv
+    dos2unix -n ${file_outputs} internal_outputAZODYN.csv
+ 
+    /bin/bash -c "Rscript --verbose /data/rAzodynSunflo.R ${crop_type} AZODYN internal_inputAZODYN.csv internal_outputAZODYN.csv \${GALAXY_SLOTS:-2}";
     zip temp_results.zip  simresults_*.txt;
     cp temp_results.zip ${simresults};
   </command>