Mercurial > repos > petr-novak > long_reads_sampling
changeset 2:ccaedca97e5e draft
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
| author | petr-novak |
|---|---|
| date | Fri, 08 Dec 2023 09:17:46 +0000 |
| parents | 5596bafd2119 |
| children | 9819570dc020 |
| files | __init__.py __pycache__/long2short.cpython-34.pyc __pycache__/long2short.cpython-35.pyc __pycache__/long2short.cpython-36.pyc galaxy_integration.org long_reads_sampling.py long_reads_sampling.xml test |
| diffstat | 6 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/galaxy_integration.org Tue Dec 12 04:33:04 2017 -0500 +++ b/galaxy_integration.org Fri Dec 08 09:17:46 2023 +0000 @@ -66,3 +66,9 @@ # it requires planemo server running! planemo shed_create --shed_target local #+END_SRC + +# create tarball which can be uploaded to repository manualy + +#+BEGIN_SRC sh +planemo shed_build . +#+END_SRC
--- a/long_reads_sampling.py Tue Dec 12 04:33:04 2017 -0500 +++ b/long_reads_sampling.py Fri Dec 08 09:17:46 2023 +0000 @@ -57,7 +57,6 @@ cummulative_length += seq_summary.id_length[seq_id] if cummulative_length >= args.total_length: break - print(selected_seq_id) # to make it efficient same orger is necesary selected_seq_id_ordered = [i for i in seq_summary.id_length @@ -91,6 +90,9 @@ file=sys.stderr) sys.exit(1) + print("input sequence info") + print("total length: ", seq_summary.total_length) + print("number of sequences: ", seq_summary.number_of_sequence) make_sequence_sample(args, seq_summary)
--- a/long_reads_sampling.xml Tue Dec 12 04:33:04 2017 -0500 +++ b/long_reads_sampling.xml Fri Dec 08 09:17:46 2023 +0000 @@ -2,6 +2,7 @@ <requirements> <requirement type="package">biopython</requirement> <requirement type="package" version="3.6" >python</requirement> + <requirement type="literal" path="long2short.py"/> </requirements> <command detect_errors="exit_code"><![CDATA[ python3 $__tool_directory__/long_reads_sampling.py -i "$input1" -o "$output1" -l ${total_length} -s ${seed}