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comparison rp2paths.xml @ 5:bdde1d9dfaee draft

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planemo upload for repository https://github.com/brsynth/rp2paths commit 46a1a47f6df15ce1873cde96c84b11d8a4544413
author tduigou
date Wed, 24 Jul 2024 08:44:12 +0000
parents fb5a3bd084a8
children 6b2ae398f4b0
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4:850412516a46 5:bdde1d9dfaee
1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT"> 1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
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>
15 mkdir out && 15 mkdir out &&
16 python -m rp2paths all 16 python -m rp2paths all
17 '$rp2_pathways' 17 '$rp2_pathways'
18 --outdir out 18 --outdir out
19 --timeout '$adv.timeout' && 19 --timeout '$adv.timeout' &&
20 cp out/compounds.txt '$compounds' && 20 mv out/compounds.txt out/compounds.tsv &&
21 cp out/compounds.tsv '$compounds' &&
21 if test -f 'out/out_paths.csv'; then 22 if test -f 'out/out_paths.csv'; then
22 cp out/out_paths.csv '$master_pathways'; 23 cp out/out_paths.csv '$master_pathways';
23 fi 24 fi
24 ]]></command> 25 ]]></command>
25 <inputs> 26 <inputs>
43 <help><![CDATA[ 44 <help><![CDATA[
44 RP2paths 45 RP2paths
45 ======== 46 ========
46 47
47 48
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://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. 49 **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.
49
50
51 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>`_.
52 50
53 51
54 .. image:: ${static_path}/images/enumerated_pathways.png 52 .. image:: ${static_path}/images/enumerated_pathways.png
55 :width: 40 % 53 :width: 40 %
56 :align: center 54 :align: center