Mercurial > repos > tduigou > get_sbml_model

annotate get_sbml_model.xml @ 3:f59e65c1606a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Sat, 29 Apr 2023 16:44:33 +0000
parents fa893f77dc22
children 1482291aaa5c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
2 <description>Get an SBML model (BiGG)</description>
0
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
3 <requirements>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
4 <requirement type="package" version="7.81.0">curl</requirement>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
5 <requirement type="package" version="1.11">gzip</requirement>
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
6 <requirement type="package" version="5.19.2">python-libsbml</requirement>
3
f59e65c1606a planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
tduigou
parents: 2
diff changeset
7 <requirement type="package" version="5.19.2">requests</requirement>
0
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
8 </requirements>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
11 | gunzip > '$model';
2
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
12 python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
0
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
13 ]]></command>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 <inputs>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
15 <param name="input" type="select" label="Strain">
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
16 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
17 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
20 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
21 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
22 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
23 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
24 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
29 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 <option value="Recon3D">Homo sapiens (Recon3D)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
34 <option value="RECON1">Homo sapiens (RECON1)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
35 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 <option value="iMM1415">Mus musculus (iMM1415)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
39 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
41 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
49 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
50 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
58 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
63 </param>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64 </inputs>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65 <outputs>
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
66 <data name="model" format="sbml" label="${input}" />
2
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
67 <data name="taxid" format="tsv" label="${input} (taxon id)" />
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
68 <data name="compartments" format="tsv" label="${input} (compartments)" />
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
69 <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
0
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70 </outputs>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71 <tests>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 <test>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73 <!-- test 1: check if identical outputs are produced with iML1515 model input -->
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 <param name="input" value="iML1515" />
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
75 <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
2
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
76 <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
77 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
78 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
0
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 </test>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80 </tests>
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
81 <help><![CDATA[
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
82 Pick SBML Model
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
83 =================
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
84
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
85 Download the selected SBML model fromg BiGG database.
4797d0b36ff3 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86 ]]></help>
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
87 <creator>
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
88 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
89 </creator>
2
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
90 <citations>
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
91 <citation type="bibtex">
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
92 @unpublished{get_sbml_model
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
93 author = {Joan Hérisson},
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
94 title = {{get_sbml_model}},
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
95 url = {https://github.com/brsynth/},
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
96 }
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
97 </citation>
fa893f77dc22 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
tduigou
parents: 1
diff changeset
98 </citations>
1
ceffb29b60c9 planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
tduigou
parents: 0
diff changeset
99 </tool>