Mercurial > repos > tduigou > rpextractsink

annotate rpextractsink.xml @ 1:ceab7bc46740 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 03 Jan 2022 15:34:21 +0000
parents
children 8d16a0f08d0a
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1 <tool id="rpExtractSink" name="Sink from SBML" version="5.11.1">
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2 <description>Generate the RetroPath2.0 sink file from an SBML input</description>
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3 <requirements>
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4 <requirement type="package" version="5.11.1">rptools</requirement>
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5 </requirements>
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6 <stdio>
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7 <regex match="Could not retreive any species in the compartment" level="fatal" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if str($input_strain_type.strain_type) == "BiGG":
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11 curl http://bigg.ucsd.edu/static/models/$(input_strain_type.input).xml.gz --output $(input_strain_type.input).xml.gz;
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12 python -m rptools.rpextractsink
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13 $(input_strain_type.input).xml.gz
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14 #else
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15 python -m rptools.rpextractsink
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16 $(input_strain_type.input)
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17 #end if
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18 '$sink'
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19 --compartment_id '$adv.compartment_id'
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20 #if str($adv.remove_dead_end) == "true":
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21 --remove_dead_end
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22 #end if
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23 ]]></command>
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24 <inputs>
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25 <conditional name="input_strain_type">
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26 <param name="strain_type" type="select" label="Input type">
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27 <option value="BiGG" selected="true">BiGG database</option>
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28 <option value="user">Custom file</option>
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29 </param>
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30 <when value="user">
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31 <param name="input" type="data" format="sbml" optional="false" label="Strain" />
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32 </when>
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33 <when value="BiGG">
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34 <param name="input" type="select" label="Strain">
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35 <option value="iCN718">(iCN718) Acinetobacter baumannii AYE</option>
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36 <option value="iYO844">(iYO844) Bacillus subtilis subsp. subtilis str. 168</option>
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37 <option value="iRC1080">(iRC1080) Chlamydomonas reinhardtii</option>
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38 <option value="iCN900">(iCN900) Clostridioides difficile 630</option>
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39 <option value="iHN637">(iHN637) Clostridium ljungdahlii DSM 13528</option>
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40 <option value="iCHOv1_DG44">(iCHOv1_DG44) Cricetulus griseus</option>
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41 <option value="iCHOv1">(iCHOv1) Cricetulus griseus</option>
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42 <option value="iAF1260b">(iAF1260b) Escherichia coli str. K-12 substr. MG1655</option>
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43 <option value="iAF1260">(iAF1260) Escherichia coli str. K-12 substr. MG1655</option>
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44 <option value="iML1515" selected="true">(iML1515) Escherichia coli str. K-12 substr. MG1655</option>
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45 <option value="iJO1366">(iJO1366) Escherichia coli str. K-12 substr. MG1655</option>
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46 <option value="iJR904">(iJR904) Escherichia coli str. K-12 substr. MG1655</option>
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47 <option value="e_coli_core">(e_coli_core) Escherichia coli str. K-12 substr. MG1655</option>
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48 <option value="iAF987">(iAF987) Geobacter metallireducens GS-15</option>
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49 <option value="iIT341">(iIT341) Helicobacter pylori 26695</option>
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50 <option value="iAT_PLT_636">(iAT_PLT_636) Homo sapiens</option>
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51 <option value="Recon3D">(Recon3D) Homo sapiens</option>
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52 <option value="iAB_RBC_283">(iAB_RBC_283) Homo sapiens</option>
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53 <option value="RECON1">(RECON1) Homo sapiens</option>
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54 <option value="iYL1228">(iYL1228) Klebsiella pneumoniae subsp. pneumoniae MGH 78578</option>
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55 <option value="iNF517">(iNF517) Lactococcus lactis subsp. cremoris MG1363</option>
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56 <option value="iAF692">(iAF692) Methanosarcina barkeri str. Fusaro</option>
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57 <option value="iMM1415">(iMM1415) Mus musculus</option>
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58 <option value="iNJ661">(iNJ661) Mycobacterium tuberculosis H37Rv</option>
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59 <option value="iEK1008">(iEK1008) Mycobacterium tuberculosis H37Rv</option>
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60 <option value="iLB1027_lipid">(iLB1027_lipid) Phaeodactylum tricornutum CCAP 1055/1</option>
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61 <option value="iAM_Pb448">(iAM_Pb448) Plasmodium berghei</option>
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62 <option value="iAM_Pc455">(iAM_Pc455) Plasmodium cynomolgi strain B</option>
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63 <option value="iAM_Pf480">(iAM_Pf480) Plasmodium falciparum 3D7</option>
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64 <option value="iAM_Pk459">(iAM_Pk459) Plasmodium knowlesi strain H</option>
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65 <option value="iAM_Pv461">(iAM_Pv461) Plasmodium vivax Sal-1</option>
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66 <option value="iJN746">(iJN746) Pseudomonas putida KT2440</option>
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67 <option value="iJN1463">(iJN1463) Pseudomonas putida KT2440</option>
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68 <option value="iND750">(iND750) Saccharomyces cerevisiae S288C</option>
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69 <option value="iMM904">(iMM904) Saccharomyces cerevisiae S288C</option>
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70 <option value="STM_v1_0">(STM_v1_0) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2</option>
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71 <option value="iYS1720">(iYS1720) Salmonella pan-reactome</option>
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72 <option value="iSB619">(iSB619) Staphylococcus aureus subsp. aureus N315</option>
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73 <option value="iYS854">(iYS854) Staphylococcus aureus subsp. aureus USA300_TCH1516</option>
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74 <option value="iJB785">(iJB785) Synechococcus elongatus PCC 7942</option>
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75 <option value="iJN678">(iJN678) Synechocystis sp. PCC 6803</option>
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76 <option value="iSynCJ816">(iSynCJ816) Synechocystis sp. PCC 6803</option>
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77 <option value="iLJ478">(iLJ478) Thermotoga maritima MSB8</option>
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78 <option value="iIS312">(iIS312) Trypanosoma cruzi Dm28c</option>
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79 <option value="iIS312_Trypomastigote">(iIS312_Trypomastigote) Trypanosoma cruzi Dm28c</option>
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80 <option value="iIS312_Epimastigote">(iIS312_Epimastigote) Trypanosoma cruzi Dm28c</option>
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81 <option value="iIS312_Amastigote">(iIS312_Amastigote) Trypanosoma cruzi Dm28c</option>
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82 </param>
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83 </when>
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84 </conditional>
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85 <!-- <param name="input" type="data" format="sbml" optional="false" label="SBML model" /> -->
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86 <section name="adv" title="Advanced Options" expanded="false">
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87 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" />
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88 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
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89 </section>
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90 </inputs>
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91 <outputs>
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92 <data name="sink" format="csv" label="${tool.name} - ${input_strain_type.input}" />
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93 </outputs>
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94 <tests>
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95 <test>
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96 <!-- test 1: check if identical outputs are produced with default parameters -->
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97 <conditional name="input_strain_type">
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98 <param name="strain_type" value="user"/>
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99 <param name="input" value="E.coli.sbml" />
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100 </conditional>
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101 <param name="compartment_id" value="MNXC3"/>
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102 <output name="sink" file="sink.csv" ftype="csv" compare="diff"/>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106
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107 Sink from SBML
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108 =================
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109
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110 Sink refers to the collection of chemical species used by the restrosynthesis algorithm of RetroPath2.0 to finish metabolic route exploration. This tool uses an SBML file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytoplasm, Golgi apparatus, nucleus, etc) and uses its MIRIAM annotation to find their InChI structures. You can use "Remove dead-end metabolites using FVA evaluation? to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network.
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111
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112 In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is MNXC3, the MetaNetX code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed.
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113
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114 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input.
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115
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116
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117 Input
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118 -----
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119
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120 Required:
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121
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122 * **input_sbml**\ : (string) Path to the input SBML file
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123
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124 Advanced options:
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125
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126 * **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
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127 * **compartment_id**\ : (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files
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128
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129 Output
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130 ------
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131
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132 * **output_sink**\ : (string) Path to the output csv file
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133
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134
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135 Project Links
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136 ---------------------
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137
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138 * `GitHub <https://github.com/brsynth/rptools>`_
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139
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140 Version
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141 ----------
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142
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143 5.9.2
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144
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145
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146 Authors
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147 -------
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148
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149
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150 * **Melchior du Lac**
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151 * Joan Hérisson
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152
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153 License
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154 -------
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155
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156 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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157
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158 Acknowledgments
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159 ---------------
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160
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161
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162 * Thomas Duigou
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163
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164
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165
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166 ]]></help>
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167 <citations>
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168 <citation type="bibtex">
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169 @article{le2005minimum,
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170 title={Minimum information requested in the annotation of biochemical models (MIRIAM)},
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171 author={Le Nov{\`e}re, Nicolas and Finney, Andrew and Hucka, Michael and Bhalla, Upinder S and Campagne, Fabien and Collado-Vides, Julio and Crampin, Edmund J and Halstead, Matt and Klipp, Edda and Mendes, Pedro and others},
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172 journal={Nature biotechnology},
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173 volume={23},
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174 number={12},
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175 pages={1509--1515},
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176 year={2005},
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177 publisher={Nature Publishing Group}
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178 }
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179 </citation>
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180 <citation type="bibtex">
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181 @article{delepine2018retropath2,
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182 title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers},
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183 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
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184 journal={Metabolic engineering},
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185 volume={45},
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186 pages={158--170},
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187 year={2018},
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188 publisher={Elsevier}}
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189 </citation>
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190 <citation type="bibtex">
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191 @article{ebrahim2013cobrapy,
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192 title={COBRApy: COnstraints-based reconstruction and analysis for python},
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193 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
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194 journal={BMC systems biology},
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195 volume={7},
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196 number={1},
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197 pages={74},
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198 year={2013},
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199 publisher={Springer}
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200 }
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201 </citation>
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202 <citation type="bibtex">
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203 @article{bornstein2008libsbml,
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204 title={LibSBML: an API library for SBML},
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205 author={Bornstein, Benjamin J and Keating, Sarah M and Jouraku, Akiya and Hucka, Michael},
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206 journal={Bioinformatics},
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207 volume={24},
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208 number={6},
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209 pages={880--881},
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210 year={2008},
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211 publisher={Oxford University Press}
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212 }
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213 </citation>
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214 </citations>
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215 </tool>