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comparison toolfactory/README.md @ 41:f8c1694190f0 draft

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author fubar
date Sun, 16 Aug 2020 08:11:10 -0400
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40:51fa77152988 41:f8c1694190f0
1 Note as at August 8 2020 1 Note as at August 8 2020
2
3 Until a PR is accepted, galaxyxml requires a small tweak - you will need to install
4 ```
5 https://github.com/fubar2/galaxyxml
6 ```
7 instead into the virtualenv used to run galaxy and when using planemo, the
8
9 ```
10 --skip_venv
11 ```
12
13 flag must be used.
14 2
15 3
16 *WARNING before you start* 4 *WARNING before you start*
17 5
18 Install this tool on a private Galaxy ONLY 6 Install this tool on a private Galaxy ONLY
19 Please NEVER on a public or production instance 7 Please NEVER on a public or production instance
20 8
21 Updated august 2014 by John Chilton adding citation support
22
23 Updated august 8 2014 to fix bugs reported by Marius van den Beek
24
25 Please cite the resource at 9 Please cite the resource at
26 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref 10 http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
27 if you use this tool in your published work. 11 if you use this tool in your published work.
28 12
29 **Short Story** 13 **Short Story**
35 writing a single new data set as output. 19 writing a single new data set as output.
36 20
37 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters* 21 *You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*
38 22
39 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool. 23 It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.
40
41 24
42 **Automated generation of new Galaxy tools for installation into any Galaxy** 25 **Automated generation of new Galaxy tools for installation into any Galaxy**
43 26
44 A test is generated using small sample test data inputs and parameter settings you supply. 27 A test is generated using small sample test data inputs and parameter settings you supply.
45 Once the test case outputs have been produced, they can be used to build a 28 Once the test case outputs have been produced, they can be used to build a
69 can be generated. Select the "generate" option and supply some help text and 52 can be generated. Select the "generate" option and supply some help text and
70 names. The new tool will be generated in the form of a new Galaxy datatype 53 names. The new tool will be generated in the form of a new Galaxy datatype
71 *tgz* - as the name suggests, it's an archive ready to upload to a 54 *tgz* - as the name suggests, it's an archive ready to upload to a
72 Galaxy ToolShed as a new tool repository. 55 Galaxy ToolShed as a new tool repository.
73 56
74 Until tgz is added to the galaxy distribution datatypes you will need to add the following:
75 <datatype extension="tgz" type="galaxy.datatypes.binary:Binary" subclass="true" mimetype="multipart/x-gzip" display_in_upload="true" />
76
77 to::
78 [galaxyroot]/config/datatypes_conf.xml
79 57
80 Once it's in a ToolShed, it can be installed into any local Galaxy server 58 Once it's in a ToolShed, it can be installed into any local Galaxy server
81 from the server administrative interface. 59 from the server administrative interface.
82 60
83 Once the new tool is installed, local users can run it - each time, the script 61 Once the new tool is installed, local users can run it - each time, the script
127 be lack of appropriate technical skills. 105 be lack of appropriate technical skills.
128 106
129 **What it does** 107 **What it does**
130 108
131 This is a tool factory for simple scripts in python, R and 109 This is a tool factory for simple scripts in python, R and
132 perl currently. Functional tests are automatically generated. How cool is that. 110 perl currently. Functional tests are automatically generated.
133 111
134 LIMITED to simple scripts that read one input from the history. Optionally can 112 LIMITED to simple scripts that read one input from the history. Optionally can
135 write one new history dataset, and optionally collect any number of outputs 113 write one new history dataset, and optionally collect any number of outputs
136 into links on an autogenerated HTML index page for the user to navigate - 114 into links on an autogenerated HTML index page for the user to navigate -
137 useful if the script writes images and output files - pdf outputs are shown 115 useful if the script writes images and output files - pdf outputs are shown