comparison rp2paths.xml @ 6:016ae4a7705e draft default tip

planemo upload for repository https://github.com/brsynth/rp2paths commit 96a30e92eab3144b924fdba7b63be10b218160a7

5:f50160c17e02

        mkdir out &&
        python -m rp2paths all
        '$rp2_pathways'
        --outdir out
        --timeout '$adv.timeout' &&
        cp out/compounds.txt '$compounds' &&
        if test -f 'out/out_paths.csv'; then
            cp out/out_paths.csv '$master_pathways';
        fi
    ]]></command>
    <inputs>

    <help><![CDATA[
RP2paths
========


**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>`_.


.. image:: ${static_path}/images/enumerated_pathways.png
    :width: 40 %
    :align: center

6:016ae4a7705e

        mkdir out &&
        python -m rp2paths all
        '$rp2_pathways'
        --outdir out
        --timeout '$adv.timeout' &&
        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
    ]]></command>
    <inputs>

    <help><![CDATA[
RP2paths
========


**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
    :width: 40 %
    :align: center