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comparison rpextractsink.xml @ 2:8d16a0f08d0a draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 11 Jan 2022 10:26:50 +0000
parents ceab7bc46740
children 47bb93e7832b
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1:ceab7bc46740 2:8d16a0f08d0a
1 <tool id="rpExtractSink" name="Sink from SBML" version="5.11.1"> 1 <tool id="rpextractsink" name="Sink from SBML" version="5.11.1" profile="19.09">
2 <description>Generate the RetroPath2.0 sink file from an SBML input</description> 2 <description>Generate the RetroPath2.0 sink file from an SBML input</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.11.1">rptools</requirement> 4 <requirement type="package" version="5.11.1">rptools</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <regex match="Could not retreive any species in the compartment" level="fatal" /> 7 <regex match="Could not retreive any species in the compartment" level="fatal" />
8 </stdio> 8 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #if str($input_strain_type.strain_type) == "BiGG": 10 python -m rptools.rpextractsink
11 curl http://bigg.ucsd.edu/static/models/$(input_strain_type.input).xml.gz --output $(input_strain_type.input).xml.gz; 11 '$input'
12 python -m rptools.rpextractsink
13 $(input_strain_type.input).xml.gz
14 #else
15 python -m rptools.rpextractsink
16 $(input_strain_type.input)
17 #end if
18 '$sink' 12 '$sink'
19 --compartment_id '$adv.compartment_id' 13 --compartment_id '$adv.compartment_id'
20 #if str($adv.remove_dead_end) == "true": 14 #if str($adv.remove_dead_end) == "true":
21 --remove_dead_end 15 --remove_dead_end
22 #end if 16 #end if
23 ]]></command> 17 ]]></command>
24 <inputs> 18 <inputs>
25 <conditional name="input_strain_type"> 19 <param name="input" type="data" format="xml" optional="false" label="Strain" />
26 <param name="strain_type" type="select" label="Input type">
27 <option value="BiGG" selected="true">BiGG database</option>
28 <option value="user">Custom file</option>
29 </param>
30 <when value="user">
31 <param name="input" type="data" format="sbml" optional="false" label="Strain" />
32 </when>
33 <when value="BiGG">
34 <param name="input" type="select" label="Strain">
35 <option value="iCN718">(iCN718) Acinetobacter baumannii AYE</option>
36 <option value="iYO844">(iYO844) Bacillus subtilis subsp. subtilis str. 168</option>
37 <option value="iRC1080">(iRC1080) Chlamydomonas reinhardtii</option>
38 <option value="iCN900">(iCN900) Clostridioides difficile 630</option>
39 <option value="iHN637">(iHN637) Clostridium ljungdahlii DSM 13528</option>
40 <option value="iCHOv1_DG44">(iCHOv1_DG44) Cricetulus griseus</option>
41 <option value="iCHOv1">(iCHOv1) Cricetulus griseus</option>
42 <option value="iAF1260b">(iAF1260b) Escherichia coli str. K-12 substr. MG1655</option>
43 <option value="iAF1260">(iAF1260) Escherichia coli str. K-12 substr. MG1655</option>
44 <option value="iML1515" selected="true">(iML1515) Escherichia coli str. K-12 substr. MG1655</option>
45 <option value="iJO1366">(iJO1366) Escherichia coli str. K-12 substr. MG1655</option>
46 <option value="iJR904">(iJR904) Escherichia coli str. K-12 substr. MG1655</option>
47 <option value="e_coli_core">(e_coli_core) Escherichia coli str. K-12 substr. MG1655</option>
48 <option value="iAF987">(iAF987) Geobacter metallireducens GS-15</option>
49 <option value="iIT341">(iIT341) Helicobacter pylori 26695</option>
50 <option value="iAT_PLT_636">(iAT_PLT_636) Homo sapiens</option>
51 <option value="Recon3D">(Recon3D) Homo sapiens</option>
52 <option value="iAB_RBC_283">(iAB_RBC_283) Homo sapiens</option>
53 <option value="RECON1">(RECON1) Homo sapiens</option>
54 <option value="iYL1228">(iYL1228) Klebsiella pneumoniae subsp. pneumoniae MGH 78578</option>
55 <option value="iNF517">(iNF517) Lactococcus lactis subsp. cremoris MG1363</option>
56 <option value="iAF692">(iAF692) Methanosarcina barkeri str. Fusaro</option>
57 <option value="iMM1415">(iMM1415) Mus musculus</option>
58 <option value="iNJ661">(iNJ661) Mycobacterium tuberculosis H37Rv</option>
59 <option value="iEK1008">(iEK1008) Mycobacterium tuberculosis H37Rv</option>
60 <option value="iLB1027_lipid">(iLB1027_lipid) Phaeodactylum tricornutum CCAP 1055/1</option>
61 <option value="iAM_Pb448">(iAM_Pb448) Plasmodium berghei</option>
62 <option value="iAM_Pc455">(iAM_Pc455) Plasmodium cynomolgi strain B</option>
63 <option value="iAM_Pf480">(iAM_Pf480) Plasmodium falciparum 3D7</option>
64 <option value="iAM_Pk459">(iAM_Pk459) Plasmodium knowlesi strain H</option>
65 <option value="iAM_Pv461">(iAM_Pv461) Plasmodium vivax Sal-1</option>
66 <option value="iJN746">(iJN746) Pseudomonas putida KT2440</option>
67 <option value="iJN1463">(iJN1463) Pseudomonas putida KT2440</option>
68 <option value="iND750">(iND750) Saccharomyces cerevisiae S288C</option>
69 <option value="iMM904">(iMM904) Saccharomyces cerevisiae S288C</option>
70 <option value="STM_v1_0">(STM_v1_0) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2</option>
71 <option value="iYS1720">(iYS1720) Salmonella pan-reactome</option>
72 <option value="iSB619">(iSB619) Staphylococcus aureus subsp. aureus N315</option>
73 <option value="iYS854">(iYS854) Staphylococcus aureus subsp. aureus USA300_TCH1516</option>
74 <option value="iJB785">(iJB785) Synechococcus elongatus PCC 7942</option>
75 <option value="iJN678">(iJN678) Synechocystis sp. PCC 6803</option>
76 <option value="iSynCJ816">(iSynCJ816) Synechocystis sp. PCC 6803</option>
77 <option value="iLJ478">(iLJ478) Thermotoga maritima MSB8</option>
78 <option value="iIS312">(iIS312) Trypanosoma cruzi Dm28c</option>
79 <option value="iIS312_Trypomastigote">(iIS312_Trypomastigote) Trypanosoma cruzi Dm28c</option>
80 <option value="iIS312_Epimastigote">(iIS312_Epimastigote) Trypanosoma cruzi Dm28c</option>
81 <option value="iIS312_Amastigote">(iIS312_Amastigote) Trypanosoma cruzi Dm28c</option>
82 </param>
83 </when>
84 </conditional>
85 <!-- <param name="input" type="data" format="sbml" optional="false" label="SBML model" /> -->
86 <section name="adv" title="Advanced Options" expanded="false"> 20 <section name="adv" title="Advanced Options" expanded="false">
87 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" /> 21 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" />
88 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" /> 22 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
89 </section> 23 </section>
90 </inputs> 24 </inputs>
91 <outputs> 25 <outputs>
92 <data name="sink" format="csv" label="${tool.name} - ${input_strain_type.input}" /> 26 <data name="sink" format="csv" label="${tool.name} - ${input.name}" />
93 </outputs> 27 </outputs>
94 <tests> 28 <tests>
95 <test> 29 <test>
96 <!-- test 1: check if identical outputs are produced with default parameters --> 30 <!-- test 1: check if identical outputs are produced with iCN718 model input -->
97 <conditional name="input_strain_type"> 31 <param name="input" value="iCN718.xml.gz" />
98 <param name="strain_type" value="user"/>
99 <param name="input" value="E.coli.sbml" />
100 </conditional>
101 <param name="compartment_id" value="MNXC3"/>
102 <output name="sink" file="sink.csv" ftype="csv" compare="diff"/> 32 <output name="sink" file="sink.csv" ftype="csv" compare="diff"/>
103 </test> 33 </test>
104 </tests> 34 </tests>
105 <help><![CDATA[ 35 <help><![CDATA[
106 36
129 Output 59 Output
130 ------ 60 ------
131 61
132 * **output_sink**\ : (string) Path to the output csv file 62 * **output_sink**\ : (string) Path to the output csv file
133 63
134
135 Project Links 64 Project Links
136 --------------------- 65 ---------------------
137 66
138 * `GitHub <https://github.com/brsynth/rptools>`_ 67 * `GitHub <https://github.com/brsynth/rptools>`_
139 68
140 Version 69 Version
141 ---------- 70 ----------
142 71
143 5.9.2 72 5.11.1
144
145 73
146 Authors 74 Authors
147 ------- 75 -------
148
149 76
150 * **Melchior du Lac** 77 * **Melchior du Lac**
151 * Joan Hérisson 78 * Joan Hérisson
152 79
153 License 80 License
156 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 83 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
157 84
158 Acknowledgments 85 Acknowledgments
159 --------------- 86 ---------------
160 87
161
162 * Thomas Duigou 88 * Thomas Duigou
163
164
165 89
166 ]]></help> 90 ]]></help>
167 <citations> 91 <citations>
168 <citation type="bibtex"> 92 <citation type="doi">10.1038/nbt1156</citation>
169 @article{le2005minimum, 93 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
170 title={Minimum information requested in the annotation of biochemical models (MIRIAM)}, 94 <citation type="doi">10.1186/1752-0509-7-74</citation>
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}, 95 <citation type="doi">10.1093/bioinformatics/btn051</citation>
172 journal={Nature biotechnology},
173 volume={23},
174 number={12},
175 pages={1509--1515},
176 year={2005},
177 publisher={Nature Publishing Group}
178 }
179 </citation>
180 <citation type="bibtex">
181 @article{delepine2018retropath2,
182 title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers},
183 author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
184 journal={Metabolic engineering},
185 volume={45},
186 pages={158--170},
187 year={2018},
188 publisher={Elsevier}}
189 </citation>
190 <citation type="bibtex">
191 @article{ebrahim2013cobrapy,
192 title={COBRApy: COnstraints-based reconstruction and analysis for python},
193 author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
194 journal={BMC systems biology},
195 volume={7},
196 number={1},
197 pages={74},
198 year={2013},
199 publisher={Springer}
200 }
201 </citation>
202 <citation type="bibtex">
203 @article{bornstein2008libsbml,
204 title={LibSBML: an API library for SBML},
205 author={Bornstein, Benjamin J and Keating, Sarah M and Jouraku, Akiya and Hucka, Michael},
206 journal={Bioinformatics},
207 volume={24},
208 number={6},
209 pages={880--881},
210 year={2008},
211 publisher={Oxford University Press}
212 }
213 </citation>
214 </citations> 96 </citations>
215 </tool> 97 </tool>