Mercurial > repos > mingchen0919 > elastic_fastq_dump
diff README.md @ 1:1aeef205e648 draft
planemo upload
| author | mingchen0919 |
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| date | Sun, 01 Apr 2018 16:48:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sun Apr 01 16:48:53 2018 -0400 @@ -0,0 +1,63 @@ +# Elastic Galaxy Tools + +* [What are Elastic Galaxy Tools](#what-are-elastic-galaxy-tools?) +* [How to use Elastic Galaxy Tools](#how-to-use-elastic-galaxy-tools?) +* [How to develop an Elastic Galaxy Tool](#how-to-develop-an-elastic-galaxy-tool?) + + [Publish a Galaxy Tool](#publish-a-galaxy-tool) + + + + +## What are Elastic Galaxy Tools? + +**Elastic Galaxy tools** is a type of Galaxy tools that have elastic user interfaces. Users can adjust the +number of input fields a tool can have, just like using a command line tool. When using a command line tool, +users can choose which (non-required) options to use. I hope Galaxy users can do the same thing, but without +actually writing any command line scripts. + + +## How to use Elastic Galaxy Tools? + +Although any (Elastic) Galaxy tool is a wrapper of a command line tool which enables performing data analysis +through web interfaces without actually writing any command line script, understanding how to read command line +manuals will help you use Elastic Galaxy tools. + +Running a command line tool is very simple. You start with the tool name, then you specify options (also called flags) +that the tool can recognize. The tool manual should tell you which options the tool can recognize. An option may or may +not have a value followed. Some options are required and some are optional. You have to use all required options to +successfully run a command line tool. However, you can use as many optional options as you want in a call of a command +line tool. + +## How to develop an Elastic Galaxy Tool? + +### Publish a Galaxy tool + +We can use the tool **planemo** to easily publish our Galaxy tools to Tool Shed or test Tool Shed. +More details can be found **[here](http://planemo.readthedocs.io/en/latest/publishing.html)**. + +* Publish to test Tool Shed + +```bash +planemo shed_create --shed_target testtoolshed +``` + +* Update tool repository in test Tool Shed + +```bash +planemo shed_update --check_diff --shed_target testtoolshed +``` + +* Publish to Tool Shed + +```bash +planemo shed_create --shed_target toolshed +``` + +* Update tool repository in Tool Shed + +```bash +planemo shed_update --check_diff --shed_target toolshed +``` + + +
