Mercurial > repos > pablocarb > synbiodesign
annotate maketool.sh @ 14:ff6c33d3a9d5 draft
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author | pablocarb |
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date | Tue, 11 Jun 2019 09:38:55 -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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7 |
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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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19 |
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20 # Generate tool backbone (additional params need to be entered manually |
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21 planemo tool_init --force \ |
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22 --id 'optbiodes' \ |
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23 --name 'OptBioDes' \ |
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24 --description 'optimal synbio design' \ |
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25 --requirement requests@2 \ |
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26 --example_command 'python $__tool_directory__/toolOptBioDes.py $input1 $output1 $output2 -server $server' \ |
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27 --example_input 'example.xlsx' \ |
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28 --example_output 'out.csv out2.csv' \ |
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29 --help_from_command 'python3 toolOptBioDes.py -h' |
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30 |
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31 # Generate tool backbone (additional params need to be entered manually |
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32 planemo tool_init --force \ |
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33 --id 'rpviz' \ |
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34 --name 'rpVisualizer' \ |
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35 --description 'Pathway visualizer' \ |
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36 --requirement libsbml \ |
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37 --requirement networkx \ |
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38 --requirement beatifulsoup4 \ |
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39 --example_command 'python $__tool_directory__/toolVisualizer.py $input1 $output1' \ |
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40 --example_input 'path.sbml' \ |
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41 --example_output 'out.html' \ |
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42 --help_from_command 'python3 toolVisualizer.py -h' |
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43 |
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44 |
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45 # Init shed repository |
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46 planemo shed_init . --force \ |
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47 --name synbiodesign \ |
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48 --owner pablocarb \ |
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49 --description 'BioCAD for Industrial Biotechnology' \ |
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50 --category 'Systems Biology' \ |
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51 --homepage_url 'https://github.com/pablocarb/galaxysynbiodesign' |
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52 |
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53 # Create repository in the toolshed |
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54 planemo shed_create \ |
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55 --shed_target toolshed \ |
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56 --shed_key_from_env TOOLSHED |
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57 |
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58 # Create repository in the toolshed |
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59 planemo shed_create \ |
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60 --shed_target testtoolshed \ |
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61 --shed_key_from_env TESTTOOLSHED |
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62 |
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63 |
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64 # Update repository in the toolshed |
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65 planemo shed_update \ |
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66 --check_diff --shed_target toolshed \ |
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67 --shed_key_from_env TOOLSHED |
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68 |
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69 # Update repository in the toolshed |
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70 planemo shed_update \ |
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71 --check_diff --shed_target testtoolshed \ |
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72 --shed_key_from_env TESTTOOLSHED |