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comparison get_sbml_model.xml @ 6:9b5947d48192 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 87a863d4074543870caef1116b8e9be58005dcdd
author tduigou
date Mon, 28 Aug 2023 14:24:48 +0000
parents 80c32f0cb716
children 8dc4d3964ab5
comparison
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5:80c32f0cb716 6:9b5947d48192
1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT"> 1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" license="MIT">
2 <description>Get an SBML model (BiGG)</description> 2 <description>Get an SBML model (BiGG)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="7.81.0">curl</requirement> 4 <requirement type="package" version="7.81.0">curl</requirement>
5 <requirement type="package" version="1.11">gzip</requirement> 5 <requirement type="package" version="1.11">gzip</requirement>
6 <requirement type="package" version="5.19.2">python-libsbml</requirement> 6 <requirement type="package" version="5.19.2">python-libsbml</requirement>
7 <requirement type="package" version="2.29">requests</requirement> 7 <requirement type="package" version="2.29">requests</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz' 10 #if str($cond_src.from_src) == 'from_bigg'
11 | gunzip > '$model'; 11 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
12 #else
13 cp '${cond_src.input_file}' '$model' &&
14 #end if
12 python '$__tool_directory__/'get_infos.py 15 python '$__tool_directory__/'get_infos.py
13 '$model' 16 '$model'
14 --hostid '$input' 17 --hostid '${cond_src.hostid}'
15 --comp '$compartments' 18 --comp '$compartments'
16 --biomass '$biomass' 19 --biomass '$biomass'
17 --taxid '$taxid' 20 --taxid '$taxid'
18 ]]></command> 21 ]]></command>
19 <inputs> 22 <inputs>
20 <param name="input" type="select" label="Strain"> 23 <conditional name="cond_src">
21 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option> 24 <param name="from_src" type="select" label="Select source">
22 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option> 25 <option value="from_bigg" selected="True">Download model from BiGG</option>
23 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option> 26 <option value="from_history">Select file from the History</option>
24 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option> 27 </param>
25 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option> 28 <when value="from_history">
26 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option> 29 <param name="hostid" type="text" help="ID of the model">
27 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option> 30 <validator type="empty_field" message="An ID is required"/>
28 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option> 31 </param>
29 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option> 32 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
30 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option> 33 </when>
31 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option> 34 <when value="from_bigg">
32 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option> 35 <param name="hostid" type="select" label="Strain">
33 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option> 36 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
34 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option> 37 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
35 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option> 38 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
36 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option> 39 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
37 <option value="Recon3D">Homo sapiens (Recon3D)</option> 40 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
38 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option> 41 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
39 <option value="RECON1">Homo sapiens (RECON1)</option> 42 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
40 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option> 43 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
41 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option> 44 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
42 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option> 45 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
43 <option value="iMM1415">Mus musculus (iMM1415)</option> 46 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
44 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option> 47 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
45 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option> 48 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
46 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option> 49 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
47 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option> 50 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
48 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option> 51 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
49 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option> 52 <option value="Recon3D">Homo sapiens (Recon3D)</option>
50 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option> 53 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
51 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option> 54 <option value="RECON1">Homo sapiens (RECON1)</option>
52 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option> 55 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
53 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option> 56 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
54 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option> 57 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
55 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option> 58 <option value="iMM1415">Mus musculus (iMM1415)</option>
56 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option> 59 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
57 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option> 60 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
58 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option> 61 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
59 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option> 62 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
60 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option> 63 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
61 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option> 64 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
62 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option> 65 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
63 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option> 66 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
64 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option> 67 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
65 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option> 68 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
66 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option> 69 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
67 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option> 70 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
68 </param> 71 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
72 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
73 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
74 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
75 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
76 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
77 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
78 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
79 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
80 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
81 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
82 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
83 </param>
84 </when>
85 </conditional>
69 </inputs> 86 </inputs>
70 <outputs> 87 <outputs>
71 <data name="model" format="sbml" label="${input}" /> 88 <data name="model" format="sbml" label="${cond_src.hostid}" />
72 <data name="taxid" format="tsv" label="${input} (taxon id)" /> 89 <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
73 <data name="compartments" format="tsv" label="${input} (compartments)" /> 90 <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
74 <data name="biomass" format="tsv" label="${input} (biomass reactions)" /> 91 <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
75 </outputs> 92 </outputs>
76 <tests> 93 <tests>
77 <test> 94 <test>
78 <!-- test 1: check if identical outputs are produced with iML1515 model input --> 95 <conditional name="cond_src">
79 <param name="input" value="iML1515" /> 96 <param name="from_src" value="from_bigg" />
80 <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/> 97 <param name="hostid" value="iML1515" />
81 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e"/> 98 </conditional>
82 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/> 99 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
83 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/> 100 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
101 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
102 <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
84 </test> 103 </test>
104 <test>
105 <conditional name="cond_src">
106 <param name="from_src" value="from_history" />
107 <param name="hostid" value="e_coli_core" />
108 <param name="input_file" value="e_coli_core.xml" />
109 </conditional>
110 <output name="model" md5="4574760460afe9e1b3388dc15f354706" />
111 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
112 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
113 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
114 </test>
85 </tests> 115 </tests>
86 <help><![CDATA[ 116 <help><![CDATA[
87 Pick SBML Model 117 Pick SBML Model
88 ================= 118 =================
89 119
90 Download the selected SBML model fromg BiGG database. 120 Download the selected SBML model fromg BiGG database or get statistics from local SBML model.
91 ]]></help> 121 ]]></help>
92 <creator> 122 <creator>
93 <organization name="BioRetroSynth" url="https://github.com/brsynth"/> 123 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
94 </creator> 124 </creator>
95 <citations> 125 <citations>