manual of possible commands (and possible parameters)?

[marwa38]

Hi team

Could you please share the manual with the possible command lines that could be used for analysis? I kindly requested to have access to the website (GUI version) as I think it is much easier?

Cheers M

[vindarbot]

Hi @marwa38 ,

All possible FROGS command tools are the .py python tools scripts availables in the app folder: https://github.com/geraldinepascal/FROGS/tree/master/app

To install and use FROGS via command lines, I let you check the FROGS and dependancies installation section in the READme: https://github.com/geraldinepascal/FROGS/blob/master/README.md

The FROGS tutorials are available here: http://frogs.toulouse.inrae.fr/html/tuto.html

You can access the manual of your tool of interest in this way:

clustering.py -h

usage: clustering.py [-h] [-p NB_CPUS] [--debug] [-v] [-d DISTANCE]
                     [--fastidious] [-n] -f INPUT_FASTA -c INPUT_COUNT
                     [-b OUTPUT_BIOM] [--output-fasta OUTPUT_FASTA]
                     [--output-compo OUTPUT_COMPO] [-l LOG_FILE]

Single-linkage clustering on sequences.

optional arguments:
  -h, --help            show this help message and exit
  -p NB_CPUS, --nb-cpus NB_CPUS
                        The maximum number of CPUs used. [Default: 1]
  --debug               Keep temporary files to debug program.
  -v, --version         show program's version number and exit

Recommended options:
  -d DISTANCE, --distance DISTANCE
                        Maximum distance between sequences in each aggregation
                        step. RECOMMENDED : d=1 in combination with
                        --fastidious option [Default: 1]
  --fastidious          use the fastidious option of swarm to refine OTU.
                        RECOMMENDED in combination with a distance equal to 1
                        (-d). it is only usable with d=1 and mutually
                        exclusive with --denoising.

other clustering option:
  -n, --denoising       denoise data by clustering read with distance=1 before
                        perform real clustering. It is mutually exclusive with
                        --fastidious.

Inputs:
  -f INPUT_FASTA, --input-fasta INPUT_FASTA
                        The sequences file (format: FASTA).
  -c INPUT_COUNT, --input-count INPUT_COUNT

To see the succession of commands in the workflow, you can access the FROGS section on the left here if you have an account on Galaxy genotool https://vm-galaxy-prod.toulouse.inrae.fr/galaxy_main/ or on IFB Galaxy instance : https://usegalaxy.fr/ First step is preprocess, then clustering, etc

Of course, it is much user-friendly to use FROGS via the Galaxy interface

I hope I answered your question

Cheers

Vincent

[marwa38]

Dear Vincent @vindarbot

Many thanks for your response, so the steps are already arranged in galaxy, which is excellent. Thanks for sharing the details about the manual, but what about the workflows for running the analysis either way (in case I will use python or galaxy)?

Thank you again Marwa

[vindarbot]

Hello @marwa38 ,

In galaxy, you can create workflow , in the " workflow " section in the top menu and then select the tools that will then be chained automatically (after selecting a tool, you can chose the paramaters, the inputs and output names, etc)

In python, you must launch the tools independently, selecting as you go the outputs of the tools as inputs for the next tools You can create a pipeline in bash with the succession of tools you want to use, if you want to automate the tasks

Did I answer your question ?

Vincent

[marwa38]

You answered my question thank you Vincent, @vindarbot Hope that there will be a workflow/pipeline/tutorial available to make a bit maybe easier to the end user. Just as an example that I am working on now: https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC2.html Thank you again Cheers Marwa

[vindarbot]

@marwa38 Actually, tutorials are under development and will be published as soon as possible : http://frogs.toulouse.inrae.fr/html/tuto.html

If you have questions / problems about FROGS galaxy or command-lines, don't hesitate to send us a mail at frogs-support@inrae.fr

Cheers (:

Vincent