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comparison 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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5:409bcbdc92c8 6:9382bc075d81
1 <tool id="CarboSeqRunRothC" name="CarboSeqRunRothC" version="1.0.0">
2 <description>To run the RothC simulator</description>
3 <requirements>
4 <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq/testcaserothc:image-rothc-1.0</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 bash -e -c "cp -r /work/csopralibs . &&
8 cp ${simulation_data} CsopraAIALInTestCase.RData &&
9 cp ${climat_data} csopralibs/data/Csopra/Climat_Csopra/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt &&
10 cp /work/csopralibs/scripts/R/testCaseRothC.r testCaseRothC.r &&
11 sed -i 's/source(\"~\/\.Rpro/homeS <- \".\" #source(\"~\/\.Rpro/' testCaseRothC.r &&
12 sed -i 's/setwd(homeS/setwd(getwd()/' testCaseRothC.r &&
13 sed -i 's/load(\"~\/tmp/load(\"\./' testCaseRothC.r &&
14 R -e \"source('./testCaseRothC.r', echo=TRUE)\" > ${log} &&
15 cp Rplots.pdf ${plot}"
16 ]]>
17 </command>
18 <inputs>
19 <param name="simulation_data" type="data" format="rdata" label="CarboSeq simulations data (rdata file)"/>
20 <param name="climat_data" type="data" format="txt" label="CarboSeq climat data (txt file)"/>
21 </inputs>
22 <outputs>
23 <data format='txt' name="log" label="CarboSeq RothC log"/>
24 <data format='pdf' name="plot" label="CarboSeq plot"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="simulation_data" value="inputs/Galaxy1-CarboSeq_simulations_data.rdata" ftype="rdata" />
29 <param name="climat_data" value="inputs/CSOPRA_CLIMAT_MOIS_SAFRAN_2416.txt" ftype="txt" />
30 <output name="plot">
31 <assert_contents>
32 <has_size value="27045" delta="100" />
33 </assert_contents>
34 </output>
35 <output name="log">
36 <assert_contents>
37 <has_line line="> simTrial$runner$run()" />
38 </assert_contents>
39 </output>
40 </test>
41
42 </tests>
43 <help>
44 the CarboSeqGetData tool
45 ========================
46
47 credits
48 -------
49
50 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
51 - Tool Maintainer: Eric Casellas eric.casellas@inrae.fr
52 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
53 - Copyright: INRAE
54 </help>
55 </tool>