Mercurial > repos > tduigou > get_sbml_model

annotate get_sbml_model.xml @ 12:1aadcfdae10b draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
author tduigou
date Tue, 01 Apr 2025 10:00:10 +0000
parents 062f51695ae0
children 6bcd8f09158d
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1 <tool id="get_sbml_model" name="Pick SBML Model" version="0.3.0" profile="21.09" license="MIT">
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2 <description>Get an SBML model (BiGG)</description>
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3 <requirements>
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4 <requirement type="package" version="7.81.0">curl</requirement>
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5 <requirement type="package" version="1.11">gzip</requirement>
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6 <requirement type="package" version="5.19.2">python-libsbml</requirement>
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7 <requirement type="package" version="2.29">requests</requirement>
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8 <requirement type="package" version="0.1.1">taxonid</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 #if str($cond_src.from_src) == 'from_bigg'
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13 curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid.hostid}.xml.gz' | gunzip > '$model' &&
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14 #else
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15 #set model=$cond_src.input_file
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16 #end if
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17 python '$__tool_directory__/'get_infos.py
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18 '$model'
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19 --hostname-or-id '$cond_src.hostid.hostid'
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20 --taxid '$taxid'
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21 --comp '$compartments'
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22 --biomass '$biomass'
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23 ]]></command>
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24 <inputs>
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25 <conditional name="cond_src">
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26 <param name="from_src" type="select" label="Select source">
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27 <option value="from_bigg" selected="True">Download model from BiGG</option>
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28 <option value="from_history">Select file from the History</option>
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29 </param>
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30 <when value="from_history">
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31 <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
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32 <section name="hostid" title="Model's ID" expanded="false">
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33 <param name="hostid" type="text" label="Model's hostname or ID" help="Model extended name or ID" optional="True"/>
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34 </section>
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35 </when>
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36 <when value="from_bigg">
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37 <section name="hostid" title="Model's ID" expanded="true">
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38 <param name="hostid" type="select" label="Strain">
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39 <!-- Be careful, the text name is used for the hostname variable -->
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40 <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
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41 <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
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42 <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
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43 <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
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44 <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
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45 <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
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46 <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
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47 <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
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48 <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
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49 <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
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50 <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
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51 <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
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52 <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
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53 <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
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54 <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
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55 <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
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56 <option value="Recon3D">Homo sapiens (Recon3D)</option>
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57 <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
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58 <option value="RECON1">Homo sapiens (RECON1)</option>
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59 <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
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60 <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
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61 <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
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62 <option value="iMM1415">Mus musculus (iMM1415)</option>
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63 <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
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64 <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
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65 <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
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66 <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
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67 <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
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68 <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
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69 <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
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70 <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
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71 <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
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72 <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
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73 <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
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74 <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
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75 <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
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76 <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
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77 <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
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78 <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
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79 <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
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80 <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
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81 <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
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82 <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
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83 <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
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84 <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
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85 <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
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86 <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
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87 </param>
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88 </section>
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89 </when>
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90 </conditional>
0
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91 </inputs>
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92 <outputs>
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93 <data name="model" format="sbml" label="${cond_src.hostid.hostid}">
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94 <filter>cond_src['from_src'] == 'from_bigg'</filter>
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95 </data>
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96 <data name="taxid" format="tsv" label="${cond_src.hostid.hostid} (taxon id)" />
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97 <data name="compartments" format="tsv" label="${cond_src.hostid.hostid} (compartments)" />
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98 <data name="biomass" format="tsv" label="${cond_src.hostid.hostid} (biomass reactions)" />
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99 </outputs>
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100 <tests>
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101 <test expect_num_outputs="4">
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102 <conditional name="cond_src">
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103 <param name="from_src" value="from_bigg" />
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104 <section name="hostid">
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105 <param name="hostid" value="iML1515" />
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106 </section>
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107 </conditional>
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108 <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
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109 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
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110 <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
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111 <output name="biomass" md5="95c0255bd5dd8753c6dde53c0f2958ea" />
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112 </test>
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113 <test expect_num_outputs="3">
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114 <conditional name="cond_src">
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115 <param name="from_src" value="from_history" />
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116 <section name="hostid">
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117 <param name="hostid" value="Escherichia coli str. K-12 substr. MG1655" />
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118 </section>
12
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119 <param name="input_file" value="e_coli_core.xml" />
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120 </conditional>
12
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121 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
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122 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
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123 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
10
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124 </test>
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125 <test expect_num_outputs="3">
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126 <conditional name="cond_src">
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127 <param name="from_src" value="from_history" />
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128 <section name="hostid">
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129 <param name="hostid" value="e_coli_core" />
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130 </section>
12
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131 <param name="input_file" value="e_coli_core.xml" />
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132 </conditional>
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133 <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
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134 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
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135 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
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136 </test>
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137 <test expect_num_outputs="3">
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138 <conditional name="cond_src">
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139 <param name="from_src" value="from_history" />
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140 <section name="hostid">
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141 <param name="hostid" value="iMM1415" />
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142 </section>
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143 <param name="input_file" value="e_coli_core.xml" />
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144 </conditional>
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145 <output name="taxid" md5="9c5ebe6ee91a632cbfb244435db7ce7e" />
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146 <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
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147 <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
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148 </test>
0
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149 </tests>
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150 <help><![CDATA[
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151 Pick SBML Model
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152 =================
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153
6
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154 Download the selected SBML model fromg BiGG database or get statistics from local SBML model.
0
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155 ]]></help>
1
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156 <creator>
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157 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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158 </creator>
2
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159 <citations>
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160 <citation type="bibtex">
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161 @unpublished{get_sbml_model
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162 author = {Joan Hérisson},
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163 title = {{get_sbml_model}},
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164 url = {https://github.com/brsynth/},
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165 }
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166 </citation>
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167 </citations>
1
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168 </tool>