annotate galaxy_integration.org @ 0:dd46956ff61f draft

Uploaded

#+TITLE: Building galaxy tools
#+BEGIN_SRC sh
# require planemo
if [ -e "long_reads_sampling.xml" ]
then
   echo "backing up original file"
   cp long_reads_sampling.xml long_reads_sampling.xml.backup
fi
planemo tool_init --force  --id 'long_reads_sampling' \
--name 'Create sample of long reads' \
--requirement biopython \
--example_command 'long_reads_sampling.py -i input_seq.fasta -o output_seq.fasta -l total_length -s seed' \
--example_input 'input_seq.fasta' \
--example_output 'output_seq.fasta'

#+END_SRC

#+RESULTS:
| backing         | up      | original | file                         |
| Tool | written | to       | long_reads_sampling.xml |

file must be manually edited

# create toolshed configuration
#+BEGIN_SRC bash
planemo shed_init --name=long_reads_sampling \
                    --owner=repeatexplorer \
                    --description=long_reads_sampling \
                    --long_description="Create sample of long reads" \
                    --category="Fasta Manipulation"
planemo shed_lint --tools
#+END_SRC

#+RESULTS:

# creating repository - once

#+BEGIN_SRC bash
# it requires planemo server running!
planemo shed_create --shed_target local
#+END_SRC