Saga Start of xml templates #1
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| <yield/> | ||
| </requirements> | ||
| </xml> | ||
| <xml name="figaro_edam"> |
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This is something I'll need on to find the right edam ontologies for figaro (I tried to find on Bio tools but it's not obvious to me which are the ontologies if they are there)
| <edam_operation>operation_TODO</edam_operation> | ||
| </edam_operations> | ||
| </xml> | ||
| <xml name="figaro_bibref"> |
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TO DO find some citation for each tools
| <requirement type="package" version="0.8.9">r-grid</requirement> | ||
| <requirement type="package" version="0.8.9">r-rcolorbrewer</requirement> | ||
| <requirement type="package" version="0.8.9">r-ggpubr</requirement> | ||
| <requirement type="package" version="0.8.9">r-ggplot2</requirement> |
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TO DO put the real version of packages (for now it's just a bad copy paste) for those with real versions I put the latest one available on anaconda.
Maybe better if I take the ones from the environment you created ?
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| ]]></command> | ||
| <inputs> | ||
| <param name="raw_data" type="data" format="" label="Raw data" help="TODO" /> |
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Not sure which format in expected here
| <container type="docker">quay.io/qiime2/amplicon:2024.10</container> | ||
| </requirements> | ||
| <version_command>q2galaxy version dbotu_q2</version_command> | ||
| <command detect_errors="exit_code">q2galaxy run dbotu_q2 call_otus '$inputs'</command> |
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This is not sure at all I just wrote the command with how I felt it could be
| <inputs name="inputs" data_style="staging_path_and_source_path"/> | ||
| </configfiles> | ||
| <inputs> | ||
| <param name="table" type="data" format="qza" label="table" help=""/> |
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Same issue I don't know the inputs and the format
same pb for the outputs I just guessed
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| ]]></command> | ||
| <inputs> | ||
| <param name="cpu" type="integer" value="0" label="CPU" help="TODO" /> |
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This should be put as default (did not find exactly how to do it in frogs fro now)
| <param name="swarm_asv_seq" type="data" format="fasta" label="ASV swarm sequences" help="TODO" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="Swarm output" format="" from_work_dir="./output_dir/*" label="${tool.name} on ${on_string} output" /> |
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I am missing the format of the output, fasta ?
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Figaro Finished and working (planemo serve and test) with the entire dataset V4 of samba.
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& start conversion json csv
Just started the work
I have put in the excel document the different comments and questions and also in purple what need to be done.
I put here also the skeleton of an eventual workflow for the Illumina part for now https://usegalaxy.eu/u/marie.josse/w/unnamed-workflow
So from this workflow you can see that I will work on the orange parts.
In this PR I will review directly the bits of code where I have question (regarding inputs, outputs and so on)
@lleroi Does this way of working fits you ? (I wanted to add some issues but I don't see the issue button in top pannel.... it's weird)