| Next changeset 1:2c788cd11881 (2021-12-02) |
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Commit message:
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added:
rp2paths/rp2paths.xml rp2paths/test-data/results_retropath2.csv rp2paths/test-data/rp2paths_compounds.tsv rp2paths/test-data/rp2paths_pathways.csv |
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| diff -r 000000000000 -r fe9607e0abba rp2paths/rp2paths.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2paths/rp2paths.xml Mon Jun 28 15:36:21 2021 +0000 |
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| @@ -0,0 +1,108 @@ +<tool id="rp2paths" name="RP2paths" version="1.4.2"> + <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> + <requirements> + <requirement type="package">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[ + #from os import path as os_path + cd /tmp && + #set outFolder = os_path.basename(str($rp2paths_pathways)) + mkdir '$outFolder' && + python -m rp2paths all + '$rp2_pathways' + --outdir '$outFolder' + --timeout '$adv.timeout' && + cp '$outFolder'/out_comp '$rp2paths_compounds' && + cp '$outFolder'/out_paths.csv '$rp2paths_pathways' && + rm -rf $outFolder + ]]></command> + <inputs> + <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="timeout" type="integer" value="1800" label="Time Out" /> + </section> + </inputs> + <outputs> + <data name="rp2paths_pathways" format="csv" label="${tool.name} Pathways" /> + <data name="rp2paths_compounds" format="tsv" label="${tool.name} Compounds" /> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced with default parameters --> + <param name="rp2_pathways" value="results_retropath2.csv" /> + <output name="rp2paths_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> + <output name="rp2paths_compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +rp2paths +======== + + +RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/rp2paths>`_. + +Input +----- + +Required information: + + +* **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file + +Advanced options: + + +* **timeout**\ : (string, default: 30 minutes) Time out time of the tool +* **server_url**\ : (string) IP address of the rp2paths REST service + +Output +------ + + +* **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest. +* **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways. + +Versioning +---------- + +v0.1 + +Authors +------- + + +* **Melchior du Lac** +* Thomas Duigou +* Baudoin Delépine +* Pablo Carbonell + +License +------- + +`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.txt>`_ + +Acknowledgments +--------------- + + +* Joan Hérisson + + ]]></help> + <citations> + <citation type="bibtex"> +@article{delepine2018retropath2, + title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers}, + author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup}, + journal={Metabolic engineering}, + volume={45}, + pages={158--170}, + year={2018}, + publisher={Elsevier}} + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r fe9607e0abba rp2paths/test-data/results_retropath2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2paths/test-data/results_retropath2.csv Mon Jun 28 15:36:21 2021 +0000 |
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| b'@@ -0,0 +1,50 @@\n+"Initial source","Transformation ID","Reaction SMILES","Substrate SMILES","Substrate InChI","Product SMILES","Product InChI","In Sink","Sink name","Diameter","Rule ID","EC number","Score","Starting Source 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| diff -r 000000000000 -r fe9607e0abba rp2paths/test-data/rp2paths_compounds.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2paths/test-data/rp2paths_compounds.tsv Mon Jun 28 15:36:21 2021 +0000 |
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| @@ -0,0 +1,1 @@ +"[CMPD_0000000003]" "[CMPD_0000000005]" "[CMPD_0000000007]" "[CMPD_0000000008]" "[CMPD_0000000009]" "[CMPD_0000000010]" "[TARGET_0000000001]" |
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| diff -r 000000000000 -r fe9607e0abba rp2paths/test-data/rp2paths_pathways.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rp2paths/test-data/rp2paths_pathways.csv Mon Jun 28 15:36:21 2021 +0000 |
| b |
| @@ -0,0 +1,64 @@ +"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_0_0","RR-02-08eb71f5bf7680a5-16-F","1.CMPD_0000000005:1.MNXM1:1.MNXM4","1.CMPD_0000000003" +"4","TRS_0_2_72_0","RR-02-ec4504ea1f031ee5-16-F","1.MNXM421","1.CMPD_0000000005" 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