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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
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0:1e7007e80a4b 1:7db06bf670db
1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09"> 1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09">
2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> 2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.5.0</token> 4 <token name="@TOOL_VERSION@">1.5.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
43 <help><![CDATA[ 43 <help><![CDATA[
44 RP2paths 44 RP2paths
45 ======== 45 ========
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48 **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. 48 **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.
49 This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis.
50 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>`_ ,
51 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.
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51 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>`_. 54 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>`_.
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