Mercurial > repos > iuc > rp2paths
changeset 0:1e7007e80a4b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c
| author | iuc |
|---|---|
| date | Mon, 17 Oct 2022 21:20:40 +0000 |
| parents | |
| children | 7db06bf670db |
| files | rp2paths.xml static/images/enumerated_pathways.png test-data/retropath2_pathways.csv test-data/rp2paths_compounds.tsv test-data/rp2paths_pathways.csv |
| diffstat | 5 files changed, 296 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2paths.xml Mon Oct 17 21:20:40 2022 +0000 @@ -0,0 +1,96 @@ +<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09"> + <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> + <macros> + <token name="@TOOL_VERSION@">1.5.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> + </requirements> + <stdio> + <regex match="TIMEOUT:" level="fatal" /> + <regex match="ERROR:" level="fatal" /> + <regex match="WARNING:" level="warning" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + mkdir out && + python -m rp2paths all + '$rp2_pathways' + --outdir out + --timeout '$adv.timeout' && + cp out/compounds.txt '$compounds' && + if test -f 'out/out_paths.csv'; then + cp out/out_paths.csv '$master_pathways'; + fi + ]]></command> + <inputs> + <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." /> + </section> + </inputs> + <outputs> + <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> + <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="rp2_pathways" value="retropath2_pathways.csv" /> + <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> + <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +RP2paths +======== + + +**RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format. + + +An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://en.wikipedia.org/wiki/Styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_. + + +.. image:: ${static_path}/images/enumerated_pathways.png + :width: 40 % + :align: center + +| + +Input +----- + +Required information: + +* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis. + +Advanced options: + +* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes. + +Output +------ + +* **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest. +* **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System). + +Project Links +--------------------- + +* `GitHub <https://github.com/brsynth/rp2paths>`_ + +License +------- + +`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_ + +Acknowledgments +--------------- + +* Joan Hérisson + + ]]></help> + <citations> + <citation type="doi">10.1016/j.ymben.2017.12.002</citation> + </citations> +</tool> \ No newline at end of file
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+"[cis,cis-muconate]","TRS_0_3_51","[H]OC(=O)c1c([H])c([H])c(N([H])O[H])c([H])c1[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c(N([H])[H])c([H])c1[H]","[H]OC(=O)c1c([H])c([H])c(N([H])O[H])c([H])c1[H]","InChI=1S/C7H7NO3/c9-7(10)5-1-3-6(8-11)4-2-5/h1-4,8,11H,(H,9,10)","[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]","InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)","1","[MNXM6]","16","[RR-02-e518cdc230f15b69-16-F]","[NOEC]","0.0","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","3" +"[cis,cis-muconate]","TRS_0_3_65","[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1[H]>>[H]OC(=O)C(OC1([H])C([H])=C(C(=O)O[H])C([H])=C([H])C1([H])O[H])=C([H])[H]","[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1[H]","InChI=1S/C7H6O3/c8-6-3-1-2-5(4-6)7(9)10/h1-4,8H,(H,9,10)","[H]OC(=O)C(OC1([H])C([H])=C(C(=O)O[H])C([H])=C([H])C1([H])O[H])=C([H])[H]","InChI=1S/C10H10O6/c1-5(9(12)13)16-8-4-6(10(14)15)2-3-7(8)11/h2-4,7-8,11H,1H2,(H,12,13)(H,14,15)","1","[MNXM337]","16","[RR-02-b64ad57dc9b584cb-16-F]","[4.1.3.45]","0.0","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","3" +"[cis,cis-muconate]","TRS_0_3_99","[H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H]>>[H]C(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H].[H]O[H]","[H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H]","InChI=1S/C8H8O2/c1-7(9)10-8-5-3-2-4-6-8/h2-6H,1H3","[H]C(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]","InChI=1S/C8H8O/c9-7-6-8-4-2-1-3-5-8/h1-5,7H,6H2","1","[MNXM473]","16","[RR-02-47fa02d2300cc64c-16-F]","[1.2.1.39, 1.2.1.5]","1.2552725051033058","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","3" +"[cis,cis-muconate]","TRS_0_3_99","[H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H]>>[H]C(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H].[H]O[H]","[H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H]","InChI=1S/C8H8O2/c1-7(9)10-8-5-3-2-4-6-8/h2-6H,1H3","[H]O[H]","InChI=1S/H2O/h1H2","1","[MNXM2]","16","[RR-02-47fa02d2300cc64c-16-F]","[1.2.1.39, 1.2.1.5]","1.2552725051033058","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","3"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp2paths_compounds.tsv Mon Oct 17 21:20:40 2022 +0000 @@ -0,0 +1,33 @@ +Compound ID Structure +CMPD_0000000003 [H]Oc1c([H])c([H])c([H])c([H])c1O[H] +CMPD_0000000005 [H]c1c([H])c([H])c(N([H])[H])c([H])c1[H] +CMPD_0000000007 [H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H] +CMPD_0000000008 [H]OC(=O)c1c([H])c([H])c([H])c([H])c1[H] +CMPD_0000000009 [H]Oc1c([H])c([H])c([H])c([H])c1[H] +CMPD_0000000010 [H]OC(=O)c1c([H])c([H])c(O[H])c(O[H])c1[H] +CMPD_0000000015 [H]OC(=O)c1c([H])c([H])c(N([H])O[H])c([H])c1[H] +CMPD_0000000020 [H]OC(=NC([H])([H])C([H])([H])SC(=O)c1c([H])c([H])c([H])c([H])c1[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H] +CMPD_0000000025 [H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1[H] +CMPD_0000000028 [H]c1c([H])c([H])c(OC(=O)C([H])([H])[H])c([H])c1[H] +MNXM1 [H+] +MNXM01 [H+] +MNXM10 [H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H] +MNXM11 [H]OP(=O)(O[H])OP(=O)(O[H])O[H] +MNXM1132 [H]OC(=O)C([H])([H])C([H])([H])C(=O)c1c([H])c([H])c([H])c([H])c1C(=O)SC([H])([H])C([H])([H])N=C(O[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H] +MNXM12 [H]OC(=NC([H])([H])C([H])([H])S[H])C([H])([H])C([H])([H])N=C(O[H])C([H])(O[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C1([H])OC([H])(n2c([H])nc3c(N([H])[H])nc([H])nc32)C([H])(O[H])C1([H])OP(=O)(O[H])O[H] +MNXM164 [H]OC(=O)c1c([H])c([H])c(O[H])c([H])c1[H] +MNXM188 [H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H] +MNXM2 [H]O[H] +MNXM25 [H]OC(=O)C([H])([H])C([H])([H])C(=O)O[H] +MNXM337 [H]OC(=O)C(OC1([H])C([H])=C(C(=O)O[H])C([H])=C([H])C1([H])O[H])=C([H])[H] +MNXM4 O=O +MNXM421 [H]OC(=O)c1c([H])c([H])c(N([H])[H])c([H])c1[H] +MNXM438 [H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H] +MNXM455 [H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1O[H] +MNXM473 [H]C(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H] +MNXM497 [H]OC(=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H] +MNXM6 [H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H] +MNXM611 [H]OC(=O)C1=C([H])C(=O)C([H])(O[H])C([H])(O[H])C1([H])[H] +MNXM76 [H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c(O[H])c([H])c1[H] +MNXM799 [H]OC(=O)C(OC1([H])C([H])=C([H])C([H])=C(C(=O)O[H])C1([H])O[H])=C([H])[H] +TARGET_0000000001 [H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rp2paths_pathways.csv Mon Oct 17 21:20:40 2022 +0000 @@ -0,0 +1,96 @@ +"Path ID","Unique ID","Rule ID","Left","Right" +"1","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"1","TRS_0_1_2_0","RR-02-9137e79005134eeb-16-F","1.MNXM188:1.MNXM4:1.MNXM6","1.CMPD_0000000003" +"2","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"2","TRS_0_1_20_0","RR-02-876f09a1ab1b55e5-16-F","1.MNXM455","1.CMPD_0000000003" +"3","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"3","TRS_0_1_9_0","RR-02-f145fec21961a59d-16-F","1.MNXM10:1.MNXM188:1.MNXM4","1.CMPD_0000000003" +"4","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"4","TRS_0_1_11_0","RR-02-1982e8dd17b0357f-16-F","1.CMPD_0000000008:1.MNXM10:1.MNXM4","1.CMPD_0000000003" +"4","TRS_0_2_42_0","RR-02-56602d66630bcfc3-16-F","1.MNXM2:1.MNXM438","1.CMPD_0000000008" +"5","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"5","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003" +"5","TRS_0_2_58_0","RR-02-7a379131479b23f9-16-F","1.MNXM76","1.CMPD_0000000009" +"6","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"6","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003" +"6","TRS_0_2_59_0","RR-02-a51b7d91cd2e9c7b-16-F","1.MNXM2:1.MNXM497","1.CMPD_0000000009" +"7","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"7","TRS_0_1_13_0","RR-02-0a885fdec2a1ff5f-16-F","1.CMPD_0000000009:1.MNXM10:1.MNXM4","1.CMPD_0000000003" +"7","TRS_0_2_60_0","RR-02-d3b162f199b260fc-16-F","1.MNXM164","1.CMPD_0000000009" +"8","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"8","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003" +"8","TRS_0_2_58_0","RR-02-7a379131479b23f9-16-F","1.MNXM76","1.CMPD_0000000009" +"9","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"9","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003" +"9","TRS_0_2_59_0","RR-02-a51b7d91cd2e9c7b-16-F","1.MNXM2:1.MNXM497","1.CMPD_0000000009" +"10","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" +"10","TRS_0_1_16_0","RR-02-f499af41ee160034-16-F","1.CMPD_0000000009:1.MNXM4","1.CMPD_0000000003" +"10","TRS_0_2_60_0","RR-02-d3b162f199b260fc-16-F","1.MNXM164","1.CMPD_0000000009" +"11","TRS_0_0_0_0","RR-02-a0cc0be463ff412f-16-F","1.CMPD_0000000003:1.MNXM4","1.TARGET_0000000001" 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