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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 11 Jan 2022 16:15:04 +0000
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1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.1" profile="19.09">
2 <description>Pick an SBML model among a list</description>
3 <requirements>
4 <requirement type="package" version="7.81.0">curl</requirement>
5 <requirement type="package" version="1.11">gzip</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
9 | gunzip > '$sbml_model'
10 ]]></command>
11 <inputs>
12 <param name="input" type="select" label="Strain">
13 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
14 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
15 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
16 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
17 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
18 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
19 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
20 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
21 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
22 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
23 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
24 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
25 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
26 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
27 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
28 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
29 <option value="Recon3D">Homo sapiens (Recon3D)</option>
30 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
31 <option value="RECON1">Homo sapiens (RECON1)</option>
32 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
33 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
34 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
35 <option value="iMM1415">Mus musculus (iMM1415)</option>
36 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
37 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
38 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
39 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
40 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
41 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
42 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
43 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
44 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
45 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
46 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
47 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
48 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
49 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
50 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
51 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
52 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
53 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
54 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
55 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
56 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
57 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
58 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
59 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
60 </param>
61 </inputs>
62 <outputs>
63 <data name="sbml_model" format="xml" label="${tool.name} - ${input}" />
64 </outputs>
65 <tests>
66 <test>
67 <!-- test 1: check if identical outputs are produced with iML1515 model input -->
68 <param name="input" value="iML1515" />
69 <output name="sbml_model" md5="9bf81d20cab5476700697ded95b716d1"/>
70 </test>
71 </tests>
72 <help><![CDATA[
73 Pick SBML Model
74 =================
75
76 Download the selected SBML model fromg BiGG database.
77
78
79 Version
80 ----------
81 0.0.1
82
83
84 Authors
85 -------
86
87 * Joan Hérisson
88
89
90 License
91 -------
92
93 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
94
95
96 Acknowledgments
97 ---------------
98
99 * Kenza Bazi-Kabbaj
100
101 ]]></help>
102 </tool>