Mercurial > repos > petr-novak > long_reads_sampling
annotate galaxy_integration.org @ 4:060fc04af21c draft default tip
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit dcff0045d0b212ebc5c4bef6a824bdbd3bb16ac3
| author | petr-novak |
|---|---|
| date | Fri, 08 Dec 2023 13:11:02 +0000 |
| parents | ccaedca97e5e |
| children |
| rev | line source |
|---|---|
| 0 | 1 #+TITLE: Building galaxy tools |
| 1 | 2 * Long reads sampling |
| 0 | 3 #+BEGIN_SRC sh |
| 4 # require planemo | |
| 5 if [ -e "long_reads_sampling.xml" ] | |
| 6 then | |
| 7 echo "backing up original file" | |
| 8 cp long_reads_sampling.xml long_reads_sampling.xml.backup | |
| 9 fi | |
| 10 planemo tool_init --force --id 'long_reads_sampling' \ | |
| 11 --name 'Create sample of long reads' \ | |
| 12 --requirement biopython \ | |
| 13 --example_command 'long_reads_sampling.py -i input_seq.fasta -o output_seq.fasta -l total_length -s seed' \ | |
| 14 --example_input 'input_seq.fasta' \ | |
| 15 --example_output 'output_seq.fasta' | |
| 16 | |
| 17 #+END_SRC | |
| 18 | |
| 19 #+RESULTS: | |
| 20 | backing | up | original | file | | |
| 21 | [32m[1mTool | written | to | long_reads_sampling.xml[0m | | |
| 22 | |
| 1 | 23 |
| 24 | |
| 25 | |
| 26 * Short read simulator | |
| 27 #+BEGIN_SRC sh | |
| 28 # require planemo | |
| 29 if [ -e "long2short.xml" ] | |
| 30 then | |
| 31 echo "backing up original file" | |
| 32 cp long2short.xml long2short.xml.backup | |
| 33 fi | |
| 34 /home/petr/anaconda3/bin/planemo tool_init --force --id 'long2short' \ | |
| 35 --name 'Get pseudo short paired end reads from long reads' \ | |
| 36 --requirement biopython \ | |
| 37 --requirement python@3.6 \ | |
| 38 --example_command 'long2short.py -i input_seq.fasta -o output_seq.fasta -cov coverage -L insert_length -l read_length' \ | |
| 39 --example_input 'input_seq.fasta' \ | |
| 40 --example_output 'output_seq.fasta' | |
| 41 | |
| 42 #+END_SRC | |
| 43 | |
| 44 #+RESULTS: | |
| 45 : Tool written to long2short.xml | |
| 46 | |
| 0 | 47 file must be manually edited |
| 48 | |
| 1 | 49 |
| 50 * create planemo repo with all tools | |
| 0 | 51 # create toolshed configuration |
| 52 #+BEGIN_SRC bash | |
| 1 | 53 /home/petr/anaconda3/bin/planemo shed_init --name=long_reads_sampling \ |
| 0 | 54 --owner=repeatexplorer \ |
| 55 --description=long_reads_sampling \ | |
| 56 --long_description="Create sample of long reads" \ | |
| 57 --category="Fasta Manipulation" | |
| 1 | 58 /home/petr/anaconda3/bin/planemo shed_lint --tools |
| 0 | 59 #+END_SRC |
| 60 | |
| 61 #+RESULTS: | |
| 62 | |
| 63 # creating repository - once | |
| 64 | |
| 65 #+BEGIN_SRC bash | |
| 66 # it requires planemo server running! | |
| 67 planemo shed_create --shed_target local | |
| 68 #+END_SRC | |
|
2
ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
69 |
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ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
70 # create tarball which can be uploaded to repository manualy |
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ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
71 |
|
ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
72 #+BEGIN_SRC sh |
|
ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
73 planemo shed_build . |
|
ccaedca97e5e
planemo upload for repository https://github.com/kavonrtep/galaxy_tools commit 2b3bc2334397749509cdf6fc432d891a09763c4f-dirty
petr-novak
parents:
1
diff
changeset
|
74 #+END_SRC |