Mercurial > repos > tduigou > rp2paths
changeset 6:016ae4a7705e draft default tip
planemo upload for repository https://github.com/brsynth/rp2paths commit 96a30e92eab3144b924fdba7b63be10b218160a7
| author | tduigou |
|---|---|
| date | Wed, 24 Jul 2024 08:42:00 +0000 |
| parents | f50160c17e02 |
| children | |
| files | rp2paths.xml |
| diffstat | 1 files changed, 3 insertions(+), 5 deletions(-) [+] |
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--- a/rp2paths.xml Wed Feb 14 15:26:56 2024 +0000 +++ b/rp2paths.xml Wed Jul 24 08:42:00 2024 +0000 @@ -17,7 +17,8 @@ '$rp2_pathways' --outdir out --timeout '$adv.timeout' && - cp out/compounds.txt '$compounds' && + mv out/compounds.txt out/compounds.tsv && + cp out/compounds.tsv '$compounds' && if test -f 'out/out_paths.csv'; then cp out/out_paths.csv '$master_pathways'; fi @@ -45,10 +46,7 @@ ======== -**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://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/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://www.sciencedirect.com/topics/chemical-engineering/styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme-commission-number>`_. +**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) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format. .. image:: ${static_path}/images/enumerated_pathways.png