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Add RetroPath2.0 carotene example
Example files have be obtained from https://www.myexperiment.org/workflows/4987.html CWL job file added by Stefan Helfrich.
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‎examples/carotene/README.md

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# RetroPath2.0 parameters for Carotene
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Below are listed the RetroPath2.0 parameters in order to reproduce the
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carotene results. See _"RetroPath2.0_tutorial"_ file for a step-by-step
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guide.
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## Parameters
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* Input
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* Pathway length: 5
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* Source: path to _"carotene/source.csv"_ file (beta-carotene)
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* Sink: path to _"carotene/sink.csv"_ file (all _E. coli_ compounds)
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* Rules: path to _"carotene/rules.csv"_ file (see __Rules__ section)
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* Output
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* Result folder: path to the desired output folder (should exists before execution)
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* Result expected
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* The generated metabolic graph (_.json_ file in the result folder) can be visualized using the Scope Viewer.
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## Rules
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Rules have been selected according to references. Below enzymes, EC numbers and
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associated MNXR IDs for each step:
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* Enzyme: GGPP synthase
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* EC number(s): 2.5.1.29
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* MetaNetX reactions: MNXR55435
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* Enzyme: phytoene synthase
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* EC number(s): 2.5.1.32
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* MetaNetX reactions: MNXR71200, MNXR70495, MNXR15602, MNXR8603, MNXR87812, MNXR67228
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* Enzyme: phytoene desaturase
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* EC number(s): 1.3.99.31, 1.3.99.28
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* MetaNetX reactions: MNXR26357, MNXR26773, MNXR26774
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* Enzyme: lycopene cyclase
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* EC number(s): 5.5.1.19
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* MetaNetX reactions: MNXR15454, MNXR16029, MNXR60336, MNXR17616, MNXR9555,
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## References:
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* PMID: 25403509
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* MetaCyc pathway ID: PWY-7393

‎examples/carotene/rules.csv

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"Rule ID","Rule","EC number","Reaction order","Diameter","Score"
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"MNXR15454_MNXM614","([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:35](-[#1:36])(-[#1:37])-[#1:38])-[#6:7](-[#1:8])=[#6:9](-[#1:10])-[#6:11]1=[#6:12](-[#6:13](-[#1:14])(-[#1:15])-[#1:16])-[#6:17](-[#1:18])(-[#1:19])-[#6:20](-[#1:21])(-[#6:23](-[#1:24])(-[#6:26]-1(-[#6:27](-[#1:28])(-[#1:29])-[#1:30])-[#6:31](-[#1:32])(-[#1:33])-[#1:34])-[#1:25])-[#1:22])>>([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:7](-[#1:8])=[#6:9](-[#1:10])-[#6:11](-[#1:25])=[#6:12](-[#6:13](-[#1:14])(-[#1:15])-[#1:16])-[#6:17](-[#1:18])(-[#1:19])-[#6:20](-[#1:21])(-[#1:22])-[#6:23](-[#1:24])=[#6:26](-[#6:27](-[#1:28])(-[#1:29])-[#1:30])-[#6:31](-[#1:32])(-[#1:33])-[#1:34])-[#6:35](-[#1:36])(-[#1:37])-[#1:38])","5.5.1.19",1,12,1000.0
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"MNXR15602_MNXM557","([#1:1]-[#6:2](-[#6:4](-[#6:7](-[#6:10](=[#6:11](-[#6:13](-[#1:14])=[#6:15](-[#1:16])-[#6:17](-[#1:18])=[#6:19](-[#6:20](-[#1:21])(-[#1:22])-[#1:23])-[#6:24](-[#1:25])(-[#1:26])-[#6:27](-[#1:28])(-[#1:29])-[#6:30](-[#1:31])=[#6:32](-[#6:33](-[#1:34])(-[#1:35])-[#1:36])-[#6:37](-[#1:38])(-[#1:39])-[#6:40](-[#1:41])(-[#1:42])-[#6:43](-[#1:44])=[#6:45](-[#6:46](-[#1:47])(-[#1:48])-[#1:49])-[#6:50](-[#6:53](-[#1:54])(-[#1:55])-[#6:56](-[#1:57])=[#6:58](-[#6:59](-[#1:60])(-[#1:61])-[#1:62])-[#6:63](-[#1:64])(-[#1:65])-[#1:66])(-[#1:51])-[#1:52])-[#1:12])-[#6:67](-[#1:68])(-[#1:69])-[#1:70])(-[#1:8])-[#1:9])(-[#1:5])-[#1:6])=[#6:3])>>([#1]-[#8]-[#15](-[#8]-[#15](-[#8]-[#1])(=[#8])-[#8]-[#6:20](-[#1:21])(-[#1:22])-[#6:15]1(-[#6:17](-[#6:33](-[#1:34])(-[#1:35])-[#1:36])(-[#6:13]-1(-[#1:14])-[#6:11](=[#6:10](-[#6:67](-[#1:69])(-[#1:68])-[#1:70])-[#6:7](-[#1:8])(-[#1:9])-[#6:4](-[#1:6])(-[#1:5])-[#6:2](-[#1:1])=[#6:3])-[#1:12])-[#6:19](-[#6:24](-[#6:27](=[#6:30](-[#6:46](-[#1:47])(-[#1:49])-[#1:48])-[#6:32](-[#1:29])(-[#6:37](-[#1:38])(-[#1:39])-[#6:40](-[#1:41])=[#6:43](-[#6:45](-[#1:42])(-[#1:44])-[#6:50](-[#1:51])(-[#1:52])-[#6:53](-[#1:54])=[#6:56](-[#6:63](-[#1:64])(-[#1:65])-[#1:66])-[#6:58](-[#1:57])(-[#1:55])-[#1])-[#6:59](-[#1:62])(-[#1:60])-[#1:61])-[#1:31])-[#1:28])(-[#1:25])-[#1:26])(-[#1:18])-[#1:23])-[#1:16])(-[#8]-[#1])=[#8])","2.5.1.32",1,12,1000.0
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"MNXR16029_MNXM1048","([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:35](-[#1:36])(-[#1:37])-[#1:38])-[#6:7](-[#1:8])=[#6:9](-[#1:10])-[#6:11]1=[#6:12](-[#6:13](-[#1:14])(-[#1:15])-[#1:16])-[#6:17](-[#1:18])(-[#1:19])-[#6:20](-[#1:21])(-[#1:22])-[#6:23](-[#1:24])(-[#1:25])-[#6:26]-1(-[#6:27](-[#1:28])(-[#1:29])-[#1:30])-[#6:31](-[#1:32])(-[#1:33])-[#1:34])>>([#1:1]-[#6:2](=[#6:3])-[#6:4](=[#6:6](-[#6:35](-[#1:37])(-[#1:38])-[#1:36])-[#6:7](=[#6:9](-[#1:10])-[#6:11](-[#1:25])=[#6:12](-[#6:13](-[#1:16])(-[#1:15])-[#1:14])-[#6:17](-[#1:19])(-[#1:18])-[#6:20](-[#1:21])(-[#1:22])-[#6:23](-[#1:24])=[#6:26](-[#6:27](-[#1:28])(-[#1:29])-[#1:30])-[#6:31](-[#1:32])(-[#1:34])-[#1:33])-[#1:8])-[#1:5])","5.5.1.19",1,12,1000.0
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"MNXR17616_MNXM10398","([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:7](-[#1:8])(-[#1:9])-[#1:10])-[#6:11](-[#1:12])(-[#1:13])-[#6:14](-[#1:15])(-[#1:16])-[#6:17]1=[#6:18](-[#6:19](-[#1:20])(-[#1:21])-[#1:22])-[#6:23](-[#1:24])(-[#1:25])-[#6:26](-[#1:27])(-[#1:28])-[#6:29](-[#1:30])(-[#1:31])-[#6:32]-1(-[#6:33](-[#1:34])(-[#1:35])-[#1:36])-[#6:37](-[#1:38])(-[#1:39])-[#1:40])>>([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:11](-[#1:12])(-[#1:13])-[#6:14](-[#1:16])(-[#1:15])-[#6:17](-[#1:31])=[#6:18](-[#6:19](-[#1:20])(-[#1:21])-[#1:22])-[#6:23](-[#1:24])(-[#1:25])-[#6:26](-[#1:27])(-[#1:28])-[#6:29](-[#1:30])=[#6:32](-[#6:33](-[#1:34])(-[#1:35])-[#1:36])-[#6:37](-[#1:38])(-[#1:39])-[#1:40])-[#6:7](-[#1:8])(-[#1:9])-[#1:10])","5.5.1.19",1,12,1000.0
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"MNXR17616_MNXM3549","([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:11](-[#1:12])(-[#1:13])-[#6:14](-[#1:15])(-[#1:16])-[#6:17](-[#1:18])=[#6:19](-[#6:20](-[#1:21])(-[#1:22])-[#1:23])-[#6:24](-[#1:25])(-[#1:26])-[#6:27](-[#1:28])(-[#1:29])-[#6:30](-[#1:31])=[#6:32](-[#6:33](-[#1:34])(-[#1:35])-[#1:36])-[#6:37](-[#1:38])(-[#1:39])-[#1:40])-[#6:7](-[#1:8])(-[#1:9])-[#1:10])>>([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#1:5])=[#6:6](-[#6:7](-[#1:8])(-[#1:9])-[#1:10])-[#6:11](-[#1:12])(-[#1:13])-[#6:14](-[#1:16])(-[#1:15])-[#6:17]1=[#6:19](-[#6:20](-[#1:21])(-[#1:22])-[#1:23])-[#6:24](-[#1:25])(-[#1:26])-[#6:27](-[#1:28])(-[#1:29])-[#6:30](-[#1:31])(-[#1:18])-[#6:32]-1(-[#6:33](-[#1:34])(-[#1:35])-[#1:36])-[#6:37](-[#1:38])(-[#1:39])-[#1:40])","5.5.1.19",1,12,1000.0
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"MNXR26357_MNXM445","([#1:1]-[#6:2](-[#6:4](-[#6:7](-[#6:10](=[#6:11](-[#6:13](=[#6:15](-[#6:17](-[#6:81](-[#1:82])(-[#1:83])-[#1:84])=[#6:18](-[#6:20](=[#6:22](-[#6:24](=[#6:25](-[#6:27](=[#6:29](-[#1:30])-[#6:31](-[#1:32])=[#6:33](-[#6:34](-[#1:35])=[#6:36](-[#1:37])-[#6:38](-[#1:39])=[#6:40](-[#6:41](-[#1:42])=[#6:43](-[#1:44])-[#6:45](-[#1:46])=[#6:47](-[#6:48](-[#1:49])(-[#1:50])-[#1:51])-[#6:52](-[#1:53])(-[#1:54])-[#6:55](-[#1:56])(-[#1:57])-[#6:58](-[#1:59])=[#6:60](-[#6:61](-[#1:62])(-[#1:63])-[#1:64])-[#6:65](-[#1:66])(-[#1:67])-[#1:68])-[#6:69](-[#1:70])(-[#1:71])-[#1:72])-[#6:73](-[#1:74])(-[#1:75])-[#1:76])-[#1:28])-[#1:26])-[#6:77](-[#1:78])(-[#1:79])-[#1:80])-[#1:23])-[#1:21])-[#1:19])-[#1:16])-[#1:14])-[#1:12])-[#6:85](-[#1:86])(-[#1:87])-[#1:88])(-[#1:8])-[#1:9])(-[#1:5])-[#1:6])=[#6:3])>>([#1]-[#6:13](-[#1:14])(-[#6:65](-[#1:67])(-[#1:66])-[#6:60](=[#6:58](-[#6:55](-[#1:57])(-[#6:52](-[#1:54])(-[#6:47](-[#6:48](-[#1:49])(-[#1:50])-[#1:51])=[#6:45](-[#6:43](-[#1:44])=[#6:41](-[#6:40](=[#6:38](-[#6:69](-[#1:71])(-[#1:70])-[#1:72])-[#6:36](-[#1:39])(-[#6:34](-[#1:35])(-[#6:33](=[#6:31](-[#6:73](-[#1:74])(-[#1:75])-[#1:76])-[#6:29](-[#1:30])(-[#1])-[#6:27](-[#1:28])(-[#6:25](-[#1:26])=[#6:24](-[#6:22](-[#1])(-[#1:23])-[#6:20](-[#6:18](=[#6:17](-[#6:81](-[#1:84])(-[#1:82])-[#1:83])-[#6:15](-[#1:16])(-[#1])-[#1])-[#1:19])(-[#1:21])-[#1])-[#6:77](-[#1:79])(-[#1:80])-[#1:78])-[#1])-[#1])-[#1:68])-[#1:37])-[#1:32])-[#1:42])-[#1:46])-[#1:53])-[#1:56])-[#1:59])-[#6:61](-[#1:62])(-[#1:64])-[#1:63])-[#6:11](-[#1:12])=[#6:10](-[#6:7](-[#1:9])(-[#1:8])-[#6:4](-[#6:2](-[#1:1])=[#6:3])(-[#1:5])-[#1:6])-[#6:85](-[#1:86])(-[#1:87])-[#1:88])","1.3.99.31",1,12,1000.0
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"MNXR26357_MNXM557","([#1:1]-[#6:2](=[#6:3])-[#6:4](-[#6:7](-[#1:8])(-[#6:10](=[#6:11](-[#6:13](-[#1:14])(-[#1:15])-[#6:16](-[#1:17])(-[#1:18])-[#6:19](=[#6:20](-[#6:22](-[#1:23])(-[#6:25](-[#1:26])(-[#6:28](-[#6:85](-[#1:86])(-[#1:87])-[#1:88])=[#6:29](-[#6:31](-[#1:32])=[#6:33](-[#6:35](=[#6:37](-[#6:38](-[#1:39])(-[#1:40])-[#1:41])-[#6:42](-[#1:43])(-[#6:45](-[#1:46])(-[#6:48](=[#6:50](-[#6:51](-[#1:52])(-[#1:53])-[#1:54])-[#6:55](-[#1:56])(-[#1:57])-[#6:58](-[#1:59])(-[#6:61](-[#1:62])=[#6:63](-[#6:68](-[#1:69])(-[#1:70])-[#6:71](-[#6:74](=[#6:76](-[#6:77](-[#1:78])(-[#1:79])-[#1:80])-[#6:81](-[#1:82])(-[#1:83])-[#1:84])-[#1:75])(-[#1:72])-[#1:73])-[#6:64](-[#1:65])(-[#1:66])-[#1:67])-[#1:60])-[#1:49])-[#1:47])-[#1:44])-[#1:36])-[#1:34])-[#1:30])-[#1:27])-[#1:24])-[#1:21])-[#6:89](-[#1:90])(-[#1:91])-[#1:92])-[#1:12])-[#6:93](-[#1:94])(-[#1:95])-[#1:96])-[#1:9])(-[#1:5])-[#1:6])>>([#1&+:15].[#1&+:49].[#1&+:57].[#1&+:60].[#1&+:69].[#1&+:73].[#1&+:83].[#1&+:84].[#1:1]-[#6:2](-[#6:4](-[#6:7](-[#6:10](=[#6:11](-[#6:13](=[#6:81](-[#6:76](-[#6:77](-[#1:79])(-[#1:80])-[#1:78])=[#6:74](-[#6:71](=[#6:68](-[#6:63](=[#6:61](-[#6:58](=[#6:55](-[#1:56])-[#6:50](-[#1:36])=[#6:48](-[#6:45](-[#1:46])=[#6:42](-[#1:44])-[#6:37](-[#1:43])=[#6:35](-[#6:33](-[#1:34])=[#6:31](-[#1:32])-[#6:29](-[#1:30])=[#6:28](-[#6:85](-[#1:86])(-[#1:87])-[#1:88])-[#6:25](-[#1:27])(-[#1:26])-[#6:22](-[#1:24])(-[#1:23])-[#6:20](-[#1:21])=[#6:19](-[#6:89](-[#1:90])(-[#1:92])-[#1:91])-[#6:16](-[#1:18])(-[#1:17])-[#1:47])-[#6:38](-[#1:40])(-[#1:39])-[#1:41])-[#6:51](-[#1:52])(-[#1:53])-[#1:54])-[#1:59])-[#1:62])-[#6:64](-[#1:67])(-[#1:65])-[#1:66])-[#1:70])-[#1:72])-[#1:75])-[#1:82])-[#1:14])-[#1:12])-[#6:93](-[#1:94])(-[#1:95])-[#1:96])(-[#1:9])-[#1:8])(-[#1:5])-[#1:6])=[#6:3])","1.3.99.31",1,12,1000.0
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10+
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13+
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14+
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15+
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16+
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17+
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18+
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