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annotate runrothc.xml @ 6:9382bc075d81 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/33995c93db6828fb0c4e4c27964bb34497cbe9fb commit 33995c93db6828fb0c4e4c27964bb34497cbe9fb-dirty"
author siwaa
date Thu, 12 May 2022 13:10:08 +0000
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6
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1 <tool id="CarboSeqRunRothC" name="CarboSeqRunRothC" version="1.0.0">
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2 <description>To run the RothC simulator</description>
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3 <requirements>
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4 <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/testcaserothc:image-rothc-1.0</container>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 bash -e -c "cp -r /work/csopralibs . &&
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8 cp ${simulation_data} CsopraAIALInTestCase.RData &&
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9 cp ${climat_data} csopralibs/data/Csopra/Climat_Csopra/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt &&
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10 cp /work/csopralibs/scripts/R/testCaseRothC.r testCaseRothC.r &&
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11 sed -i 's/source(\"~\/\.Rpro/homeS <- \".\" #source(\"~\/\.Rpro/' testCaseRothC.r &&
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12 sed -i 's/setwd(homeS/setwd(getwd()/' testCaseRothC.r &&
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13 sed -i 's/load(\"~\/tmp/load(\"\./' testCaseRothC.r &&
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14 R -e \"source('./testCaseRothC.r', echo=TRUE)\" > ${log} &&
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15 cp Rplots.pdf ${plot}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param name="simulation_data" type="data" format="rdata" label="CarboSeq simulations data (rdata file)"/>
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20 <param name="climat_data" type="data" format="txt" label="CarboSeq climat data (txt file)"/>
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21 </inputs>
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22 <outputs>
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23 <data format='txt' name="log" label="CarboSeq RothC log"/>
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24 <data format='pdf' name="plot" label="CarboSeq plot"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="simulation_data" value="inputs/Galaxy1-CarboSeq_simulations_data.rdata" ftype="rdata" />
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29 <param name="climat_data" value="inputs/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt" ftype="txt" />
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30 <output name="plot">
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31 <assert_contents>
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32 <has_size value="27045" delta="100" />
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33 </assert_contents>
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34 </output>
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35 <output name="log">
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36 <assert_contents>
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37 <has_line line="> simTrial$runner$run()" />
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38 </assert_contents>
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39 </output>
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40 </test>
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41
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42 </tests>
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43 <help>
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44 the CarboSeqGetData tool
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45 ========================
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46
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47 credits
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48 -------
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49
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50 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
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51 - Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
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52 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
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53 - Copyright: INRAE
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54 </help>
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55 </tool>