Mercurial > repos > iuc > rp2paths
changeset 1:7db06bf670db draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit b0ee2a59d0c9618c2e6b4d6732f7de7cde04a51a
| author | iuc |
|---|---|
| date | Sun, 12 Nov 2023 13:57:52 +0000 |
| parents | 1e7007e80a4b |
| children | |
| files | rp2paths.xml |
| diffstat | 1 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/rp2paths.xml Mon Oct 17 21:20:40 2022 +0000 +++ b/rp2paths.xml Sun Nov 12 13:57:52 2023 +0000 @@ -1,7 +1,7 @@ <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> + <token name="@TOOL_VERSION@">1.5.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> @@ -45,7 +45,10 @@ ======== -**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. +**RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the "RetroPath2.0 workflow" 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>`_. @@ -93,4 +96,4 @@ <citations> <citation type="doi">10.1016/j.ymben.2017.12.002</citation> </citations> -</tool> \ No newline at end of file +</tool>