annotate maketool.sh @ 1:b0b7deebb71e draft

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author pablocarb
date Mon, 29 Apr 2019 10:53:09 -0400
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1 #!/bin/bash
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2 # author: Pablo Carbonell
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3 # Create Selenzyme Galaxy tool using planemo.
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4 # --example_input reaction.csv \
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5 # --example_output out.csv \
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6 # --example_command 'python $__tool_directory__/toolSelenzyme.py $input1 $output1 -server $server' \
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8 # Generate tool backbone (additional params need to be entered manually
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9 planemo tool_init --force \
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10 --id 'selenzyme' \
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11 --name 'Selenzyme' \
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12 --description 'enzyme sequence selection from reaction template' \
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13 --requirement requests@2 \
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14 --example_command 'python $__tool_directory__/toolSelenzyme.py $input1 $output1 -server $server' \
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15 --example_input 'reaction.csv' \
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16 --example_output 'out.csv' \
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17 --doi 10.1093/bioinformatics/bty065 \
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18 --help_from_command 'python3 toolSelenzyme.py -h'
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20 # Init shed repository
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21 planemo shed_init . --force \
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22 --name synbiodesign \
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23 --owner pablocarb \
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24 --description 'BioCAD for Industrial Biotechnology' \
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25 --category 'Systems Biology' \
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26 --homepage_url 'https://github.com/pablocarb/galaxysynbiodesign'
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28 # Create repository in the toolshed
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29 planemo shed_create \
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30 --shed_target toolshed \
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31 --shed_key_from_env TOOLSHED
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33 # Update repository in the toolshed
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34 planemo shed_update \
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35 --check_diff --shed_target toolshed \
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36 --shed_key_from_env TOOLSHED
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