comparison toolfactory/README.md @ 41:f8c1694190f0 draft

Uploaded

40:51fa77152988

Note as at August 8 2020

Until a PR is accepted, galaxyxml requires a small tweak - you will need to install
```
https://github.com/fubar2/galaxyxml
```
instead into the virtualenv used to run galaxy and when using planemo, the

```
--skip_venv 
```

flag must be used.


*WARNING before you start*

 Install this tool on a private Galaxy ONLY
 Please NEVER on a public or production instance
 
Updated august 2014 by John Chilton adding citation support

Updated august 8 2014 to fix bugs reported by Marius van den Beek

Please cite the resource at
http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
if you use this tool in your published work.

**Short Story**

writing a single new data set as output.

*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*

It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.


**Automated generation of new Galaxy tools for installation into any Galaxy**

A test is generated using small sample test data inputs and parameter settings you supply.
Once the test case outputs have been produced, they can be used to build a

can be generated. Select the "generate" option and supply some help text and
names. The new tool will be generated in the form of a new Galaxy datatype
*tgz* - as the name suggests, it's an archive ready to upload to a
Galaxy ToolShed as a new tool repository.

Until tgz is added to the galaxy distribution datatypes you will need to add the following:
    <datatype extension="tgz" type="galaxy.datatypes.binary:Binary" subclass="true" mimetype="multipart/x-gzip" display_in_upload="true" />

to::
 [galaxyroot]/config/datatypes_conf.xml

Once it's in a ToolShed, it can be installed into any local Galaxy server
from the server administrative interface.

Once the new tool is installed, local users can run it - each time, the script

be lack of appropriate technical skills.

**What it does** 

This is a tool factory for simple scripts in python, R and
perl currently. Functional tests are automatically generated. How cool is that.

LIMITED to simple scripts that read one input from the history. Optionally can
write one new history dataset, and optionally collect any number of outputs
into links on an autogenerated HTML index page for the user to navigate -
useful if the script writes images and output files - pdf outputs are shown

41:f8c1694190f0

Note as at August 8 2020


*WARNING before you start*

 Install this tool on a private Galaxy ONLY
 Please NEVER on a public or production instance
 
Please cite the resource at
http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&keytype=ref
if you use this tool in your published work.

**Short Story**

writing a single new data set as output.

*You have a working r/python/perl/bash script or any executable with positional or argparse style parameters*

It can be turned into an ordinary Galaxy tool in minutes, using a Galaxy tool.

**Automated generation of new Galaxy tools for installation into any Galaxy**

A test is generated using small sample test data inputs and parameter settings you supply.
Once the test case outputs have been produced, they can be used to build a

can be generated. Select the "generate" option and supply some help text and
names. The new tool will be generated in the form of a new Galaxy datatype
*tgz* - as the name suggests, it's an archive ready to upload to a
Galaxy ToolShed as a new tool repository.


Once it's in a ToolShed, it can be installed into any local Galaxy server
from the server administrative interface.

Once the new tool is installed, local users can run it - each time, the script

be lack of appropriate technical skills.

**What it does** 

This is a tool factory for simple scripts in python, R and
perl currently. Functional tests are automatically generated. 

LIMITED to simple scripts that read one input from the history. Optionally can
write one new history dataset, and optionally collect any number of outputs
into links on an autogenerated HTML index page for the user to navigate -
useful if the script writes images and output files - pdf outputs are shown