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comparison rp2paths.xml @ 1:8b77ca41f6af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c1706f45cf4918846b73069a7e984b771605d3aa
author iuc
date Mon, 29 Sep 2025 15:41:49 +0000
parents d468c3b714e5
children a5fb27520253
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0:d468c3b714e5 1:8b77ca41f6af
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@">2.0.0</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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