annotate maketool.sh @ 14:ff6c33d3a9d5 draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5
author pablocarb
date Tue, 11 Jun 2019 09:38:55 -0400
parents bce330b97d42
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
1 #!/bin/bash
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
2 # author: Pablo Carbonell
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
3 # Create Selenzyme Galaxy tool using planemo.
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
4 # --example_input reaction.csv \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
5 # --example_output out.csv \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
6 # --example_command 'python $__tool_directory__/toolSelenzyme.py $input1 $output1 -server $server' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
7
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
8 # Generate tool backbone (additional params need to be entered manually
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
9 planemo tool_init --force \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
10 --id 'selenzyme' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
11 --name 'Selenzyme' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
12 --description 'enzyme sequence selection from reaction template' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
13 --requirement requests@2 \
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
14 --example_command 'python $__tool_directory__/toolSelenzyme.py $input1 $output1 -server $server' \
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
15 --example_input 'reaction.csv' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
16 --example_output 'out.csv' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
17 --doi 10.1093/bioinformatics/bty065 \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
18 --help_from_command 'python3 toolSelenzyme.py -h'
2
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
19
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
20 # Generate tool backbone (additional params need to be entered manually
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
21 planemo tool_init --force \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
22 --id 'optbiodes' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
23 --name 'OptBioDes' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
24 --description 'optimal synbio design' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
25 --requirement requests@2 \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
26 --example_command 'python $__tool_directory__/toolOptBioDes.py $input1 $output1 $output2 -server $server' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
27 --example_input 'example.xlsx' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
28 --example_output 'out.csv out2.csv' \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
29 --help_from_command 'python3 toolOptBioDes.py -h'
11
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
30
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
31 # Generate tool backbone (additional params need to be entered manually
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
32 planemo tool_init --force \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
33 --id 'rpviz' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
34 --name 'rpVisualizer' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
35 --description 'Pathway visualizer' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
36 --requirement libsbml \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
37 --requirement networkx \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
38 --requirement beatifulsoup4 \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
39 --example_command 'python $__tool_directory__/toolVisualizer.py $input1 $output1' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
40 --example_input 'path.sbml' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
41 --example_output 'out.html' \
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
42 --help_from_command 'python3 toolVisualizer.py -h'
bce330b97d42 planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty
pablocarb
parents: 2
diff changeset
43
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
44
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
45 # Init shed repository
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
46 planemo shed_init . --force \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
47 --name synbiodesign \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
48 --owner pablocarb \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
49 --description 'BioCAD for Industrial Biotechnology' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
50 --category 'Systems Biology' \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
51 --homepage_url 'https://github.com/pablocarb/galaxysynbiodesign'
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
52
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
53 # Create repository in the toolshed
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
54 planemo shed_create \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
55 --shed_target toolshed \
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
56 --shed_key_from_env TOOLSHED
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
57
2
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
58 # Create repository in the toolshed
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
59 planemo shed_create \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
60 --shed_target testtoolshed \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
61 --shed_key_from_env TESTTOOLSHED
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
62
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
63
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
64 # Update repository in the toolshed
0
ac027c9ace4d planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents:
diff changeset
65 planemo shed_update \
1
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
66 --check_diff --shed_target toolshed \
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
67 --shed_key_from_env TOOLSHED
b0b7deebb71e planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty
pablocarb
parents: 0
diff changeset
68
2
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
69 # Update repository in the toolshed
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
70 planemo shed_update \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
71 --check_diff --shed_target testtoolshed \
856bd14e6e96 planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
pablocarb
parents: 1
diff changeset
72 --shed_key_from_env TESTTOOLSHED