| Previous changeset 2:550f1c02caba (2022-02-22) Next changeset 4:850412516a46 (2023-05-30) |
|
Commit message:
planemo upload for repository https://github.com/brsynth/rp2paths commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3 |
|
modified:
rp2paths.xml |
|
added:
config/job_conf.xml config/tool_conf.xml static/images/enumerated_pathways.png |
| b |
| diff -r 550f1c02caba -r fb5a3bd084a8 config/job_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/job_conf.xml Mon Apr 24 13:31:01 2023 +0000 |
| b |
| @@ -0,0 +1,1 @@ + <tool id="rp2paths" destination="local" /> |
| b |
| diff -r 550f1c02caba -r fb5a3bd084a8 config/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Mon Apr 24 13:31:01 2023 +0000 |
| b |
| @@ -0,0 +1,3 @@ + <section id="sbc-rs" name="SynBioCAD RetroSynthesis"> + <tool file="synbiocad-galaxy-wrappers/rp2paths/rp2paths.xml" /> + </section> |
| b |
| diff -r 550f1c02caba -r fb5a3bd084a8 rp2paths.xml --- a/rp2paths.xml Tue Feb 22 11:12:52 2022 +0000 +++ b/rp2paths.xml Mon Apr 24 13:31:01 2023 +0000 |
| [ |
| @@ -1,106 +1,83 @@ -<tool id="rp2paths" name="RP2paths" version="1.5.0"> +<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT"> <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description> + <macros> + <token name="@TOOL_VERSION@">1.5.0</token> + </macros> <requirements> - <requirement type="package" version="1.5.0">rp2paths</requirement> + <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement> </requirements> - <stdio> + <stdio> <regex match="TIMEOUT:" level="fatal" /> <regex match="ERROR:" level="fatal" /> - <regex match="WARNING:" level="warning" /> - </stdio> + <regex match="WARNING:" level="warning" /> + </stdio> <command detect_errors="exit_code"><![CDATA[ mkdir out && python -m rp2paths all '$rp2_pathways' --outdir out --timeout '$adv.timeout' && - if test -f "out/compounds.txt"; then - cp out/compounds.txt '$compounds'; - cp out/out_paths.csv '$master_pathways'; + cp out/compounds.txt '$compounds' && + if test -f 'out/out_paths.csv'; then + cp out/out_paths.csv '$master_pathways'; fi ]]></command> <inputs> - <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" /> + <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/> <section name="adv" title="Advanced Options" expanded="false"> - <param name="timeout" type="integer" value="1800" label="Time Out" /> + <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." /> </section> </inputs> <outputs> - <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" /> - <data name="compounds" format="tsv" label="${tool.name} (Compounds)" /> + <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" /> + <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" /> </outputs> <tests> <test> <!-- test 1: check if identical outputs are produced with default parameters --> <param name="rp2_pathways" value="retropath2_pathways.csv" /> <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/> - <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/> + <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/> </test> </tests> <help><![CDATA[ -rp2paths +RP2paths ======== -RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/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 + +| Input ----- Required information: - -* **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file +* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis. Advanced options: - -* **timeout**\ : (string, default: 30 minutes) Time out time of the tool -* **server_url**\ : (string) IP address of the rp2paths REST service +* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes. Output ------ - -* **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest. -* **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways. - -Versioning ----------- - -v1.4.3 - -Authors -------- - - -* **Melchior du Lac** -* Thomas Duigou -* Baudoin Delépine -* Pablo Carbonell - -License -------- - -`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_ - -Acknowledgments ---------------- - - -* Joan Hérisson - +* **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest. +* **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System). ]]></help> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> <citations> - <citation type="bibtex"> -@article{delepine2018retropath2, - title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers}, - author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup}, - journal={Metabolic engineering}, - volume={45}, - pages={158--170}, - year={2018}, - publisher={Elsevier}} - </citation> + <citation type="doi">10.1016/j.ymben.2017.12.002</citation> </citations> -</tool> \ No newline at end of file +</tool> |
| b |
| diff -r 550f1c02caba -r fb5a3bd084a8 static/images/enumerated_pathways.png |
| b |
| Binary file static/images/enumerated_pathways.png has changed |
