Mercurial > repos > siwaa > redelac_stics_g

changeset 13:3db1f57029a7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 4a2264991516b494ed11d1a7d5260ba543696a04"
author siwaa
date Fri, 27 Oct 2023 09:17:06 +0000
parents 9f398c5117d2
children 812bb8097dac
files redelacSticsInputGenerator.bash redelacSticsInputGenerator.xml
diffstat 2 files changed, 49 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/redelacSticsInputGenerator.bash	Tue Oct 17 11:21:36 2023 +0000
+++ b/redelacSticsInputGenerator.bash	Fri Oct 27 09:17:06 2023 +0000
@@ -28,7 +28,7 @@
 echo "=================================" && 
 rm WS/1* &&
 mv WS $WSname &&
-/usr/bin/time -p -o ./bashlog zip -q -r $WSname $WSname &&
+/usr/bin/time -p -o ./bashlog zip ${13} -q -r $WSname $WSname &&
 echo "Step 2, time to zip the Workspace:" &&
 echo "==================================" && 
 cat ./bashlog &&
--- a/redelacSticsInputGenerator.xml	Tue Oct 17 11:21:36 2023 +0000
+++ b/redelacSticsInputGenerator.xml	Fri Oct 27 09:17:06 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.6">
+<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.7">
   <description>to run generate Stics Inputs for REDELAC</description>
   <requirements>
-    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:b0f76897e1ece4a91ecfc71617fec5ebd04e2bd4</container>
+    <container type="singularity">docker://registry.forgemia.inra.fr/redelac/redelac-toolbox/sticsrpacks:0faa63e7838a2b86369026bf2e628842d7af9863</container>
   </requirements>
   <command detect_errors="aggressive">
     <![CDATA[
@@ -15,7 +15,7 @@
              #else
                 parallel=parallel &&
              #end if
-	        bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace}
+	        bash $__tool_directory__/redelacSticsInputGenerator.bash ${IterUsmX.IterUsmX} \${parallel} \${GALAXY_SLOTS:-4} $__tool_directory__ ${Workspace} ${Climat} ${USMs} ${Tec} ${Ini} ${Station} \${additional} ${GeneratedWorkspace} ${compress}
      ]]>
   </command>
   <inputs>
@@ -34,6 +34,7 @@
 	<when value="usmx_at_once">
       </when>
     </conditional>
+    <param name="compress" type="boolean" checked="true" truevalue="-6" falsevalue="-0"/>
   </inputs>
   <outputs>
     <data format="zip" name="GeneratedWorkspace"
@@ -127,6 +128,50 @@
 	</assert_contents>	  
       </output>
     </test>
+    <test>
+      <param name="compress" value="false" ftype="boolean" />
+      <param name="parallel" value="true" ftype="boolean" />
+      <param name="Workspace" value="input/sticsBaseWs.zip" ftype="zip" />
+      <param name="Climat" value="input/flatMeteo.zip" ftype="zip" />    
+      <param name="USMs" value="input/USMsSheet.csv" ftype="csv" />
+      <param name="Tec" value="input/TecSheet.csv" ftype="csv" />
+      <param name="Ini" value="input/IniSheet.csv" ftype="csv"/>
+      <param name="Station" value="input/StationsSheet.csv" ftype="csv"/>
+      <output name="GeneratedWorkspace" ftype="zip" >
+	<assert_contents>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1973-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1973-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1974-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1974-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-NA-1975-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-NA-1975-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1976-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1976-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-1977-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-1977-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2000-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2000-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2001-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2001-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2002-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2002-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2003-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2003-PP" />
+	  </has_archive_member>
+	  <has_archive_member path="rot8_2\/txt_files\/806_1893-637_NPP1-8-2-PP-ref-2004-PP\/new_travail.usm">
+	    <has_text text="806_1893-637_NPP1-8-2-PP-ref-2004-PP" />
+	  </has_archive_member>
+	</assert_contents>	  
+      </output>
+    </test>
   </tests>
   <help>
 *The usage of this tool is restricted to the user of the stics_authorized group.*