Mercurial > repos > petr-novak > long_reads_sampling
diff galaxy_integration.org @ 0:dd46956ff61f draft
Uploaded
author | petr-novak |
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date | Fri, 08 Dec 2017 09:57:17 -0500 |
parents | |
children | 5596bafd2119 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_integration.org Fri Dec 08 09:57:17 2017 -0500 @@ -0,0 +1,41 @@ +#+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 | +| [32m[1mTool | written | to | long_reads_sampling.xml[0m | + +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