Mercurial > repos > siwaa > carboseq_s

annotate carboseqSimulator.xml @ 8:5fdc9d0c223b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
author siwaa
date Fri, 30 Aug 2024 13:29:48 +0000
parents 366449cab681
children 2af4b1e46d90
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
5fdc9d0c223b "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/43e7f4ebfe4e552bf684936df0a050cb6def5aab/toos/CarboSeqSimulator commit 43e7f4ebfe4e552bf684936df0a050cb6def5aab-dirty"
siwaa
parents: 7
diff changeset
1 <tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.14">
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
2 <description>To run the CarboSeq simulator</description>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
3 <requirements>
6
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
4 <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:siwaa</container>
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
5 </requirements>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
7 (env | grep DOCKER_IMAGE) &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
8 printf " Image Reg : \$s\n" \$(env | grep DOCKER_IMAGE) &&
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
9 bash -e -c "mkdir output &&
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
10 unzip -d input ${input} &&
6
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
11 cp /usr/local/src/myscripts/semantifier.jar . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
12 cp /usr/local/src/myscripts/start_server.sh . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
13 cp -r /usr/local/src/myscripts/config_mappers . &&
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
14 cp -r /usr/local/src/myscripts/data . &&
7
366449cab681 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa/toos/CarboSeqSimulator commit b4b11a86a9c43b3dd4a3d27af9f2d99463cdbffa-dirty"
siwaa
parents: 6
diff changeset
15 Rscript $__tool_directory__/run.r --srcDir=\$(realpath -s input) --srcOut=\$(realpath -s output) --semPath=\$(realpath -s .) --part=${semantifier} --NBCores=\${GALAXY_SLOTS:-4}&&
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
16 cp output/* ${output}"
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
17 ]]>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
18 </command>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
19 <inputs>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
20 <param name="input" type="data" format="zip" label="CarboSeq input (zip)"/>
6
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
21 <param name="semantifier" type="select" label="Choose the semantifier mode:">
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
22 <option value="modeltoolbox_sem_local" selected="true">local</option>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
23 <option value="modeltoolbox_sem_remote">remote</option>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
24 </param>
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
25 </inputs>
6
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
26 <outputs>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
27 <data format='rdata' name="output" label="CarboSeq output (rdata)"/>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
28 </outputs>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
29 <tests>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
30 <test>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
31 <param name="input" value="input/40Sites.zip" ftype="zip" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
32 <param name="semantifier" value="modeltoolbox_sem_local" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
33 <output name="output" ftype="rdata" >
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
34 <assert_contents>
4
a069fc43b0b1 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7/toos/CarboSeqSimulator commit ed5816b24b0c91099c78cbb5bbbe835ae5c74cd7-dirty"
siwaa
parents: 3
diff changeset
35 <has_size value="38654" negate="false" />
1
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
36 <has_size value="0" negate="true" />
89c69fcbf561 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c/toos/CarboSeqSimulator commit ae4b6513d1114f2bf0f476b9398c6d8d39e08a0c-dirty"
siwaa
parents: 0
diff changeset
37 </assert_contents>
6
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
38 </output>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
39 </test>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
40 <test>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
41 <param name="input" value="input/40Sites.zip" ftype="zip" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
42 <param name="semantifier" value="modeltoolbox_sem_remote" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
43 <output name="output" ftype="rdata" >
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
44 <assert_contents>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
45 <has_size value="38654" negate="false" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
46 <has_size value="0" negate="true" />
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
47 </assert_contents>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
48 </output>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
49 </test>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
50 </tests>
f9183e245cdb "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9/toos/CarboSeqSimulator commit e0ce824c8f8d3fa1ca5ebd32a2424f2478653ad9-dirty"
siwaa
parents: 4
diff changeset
51 <help>
0
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
52 the CarboSeq CarboseqSimulator tool
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
53 ===================================
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
54
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
55 credits
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
56 -------
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
57 - Wrapper Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
58 - Tool Site: https://forgemia.inra.fr/carboseq/record-projet-carboseq
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
59 - Copyright: INRAE
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
60 </help>
fb1b9308807f Uploaded
siwaa
parents:
diff changeset
61 </tool>