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1 #+TITLE: Building galaxy tools
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2 #+BEGIN_SRC sh
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3 # require planemo
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4 if [ -e "long_reads_sampling.xml" ]
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5 then
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6 echo "backing up original file"
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7 cp long_reads_sampling.xml long_reads_sampling.xml.backup
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8 fi
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9 planemo tool_init --force --id 'long_reads_sampling' \
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10 --name 'Create sample of long reads' \
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11 --requirement biopython \
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12 --example_command 'long_reads_sampling.py -i input_seq.fasta -o output_seq.fasta -l total_length -s seed' \
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13 --example_input 'input_seq.fasta' \
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14 --example_output 'output_seq.fasta'
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15
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16 #+END_SRC
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17
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18 #+RESULTS:
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19 | backing | up | original | file |
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20 | [32m[1mTool | written | to | long_reads_sampling.xml[0m |
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21
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22 file must be manually edited
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23
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24 # create toolshed configuration
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25 #+BEGIN_SRC bash
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26 planemo shed_init --name=long_reads_sampling \
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27 --owner=repeatexplorer \
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28 --description=long_reads_sampling \
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29 --long_description="Create sample of long reads" \
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30 --category="Fasta Manipulation"
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31 planemo shed_lint --tools
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32 #+END_SRC
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33
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34 #+RESULTS:
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35
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36 # creating repository - once
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37
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38 #+BEGIN_SRC bash
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39 # it requires planemo server running!
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40 planemo shed_create --shed_target local
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41 #+END_SRC
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