Mercurial > repos > petr-novak > long_reads_sampling

comparison galaxy_integration.org @ 1:5596bafd2119 draft

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Uploaded
author petr-novak
date Tue, 12 Dec 2017 04:33:04 -0500
parents dd46956ff61f
children ccaedca97e5e
comparison
equal deleted inserted replaced
0:dd46956ff61f 1:5596bafd2119
1 #+TITLE: Building galaxy tools 1 #+TITLE: Building galaxy tools
2 * Long reads sampling
2 #+BEGIN_SRC sh 3 #+BEGIN_SRC sh
3 # require planemo 4 # require planemo
4 if [ -e "long_reads_sampling.xml" ] 5 if [ -e "long_reads_sampling.xml" ]
5 then 6 then
6 echo "backing up original file" 7 echo "backing up original file"
17 18
18 #+RESULTS: 19 #+RESULTS:
19 | backing | up | original | file | 20 | backing | up | original | file |
20 | Tool | written | to | long_reads_sampling.xml | 21 | Tool | written | to | long_reads_sampling.xml |
21 22
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
22 file must be manually edited 47 file must be manually edited
23 48
49
50 * create planemo repo with all tools
24 # create toolshed configuration 51 # create toolshed configuration
25 #+BEGIN_SRC bash 52 #+BEGIN_SRC bash
26 planemo shed_init --name=long_reads_sampling \ 53 /home/petr/anaconda3/bin/planemo shed_init --name=long_reads_sampling \
27 --owner=repeatexplorer \ 54 --owner=repeatexplorer \
28 --description=long_reads_sampling \ 55 --description=long_reads_sampling \
29 --long_description="Create sample of long reads" \ 56 --long_description="Create sample of long reads" \
30 --category="Fasta Manipulation" 57 --category="Fasta Manipulation"
31 planemo shed_lint --tools 58 /home/petr/anaconda3/bin/planemo shed_lint --tools
32 #+END_SRC 59 #+END_SRC
33 60
34 #+RESULTS: 61 #+RESULTS:
35 62
36 # creating repository - once 63 # creating repository - once