view fastqc_checker.xml @ 0:d8d131d08779 draft default tip

Initial upload.

<tool id="fastqc_checker_1" name="FastQC checker" version="1.0.0">
	<description>for quality control of high throughput sequence data</description>

	<command interpreter="python">
		fastqc_checker.py -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc -o $output $input
	</command>

	<inputs>
		<param format="fastq" name="input" type="data" label="Source files" multiple="true"/>
	</inputs>
	<outputs>
		<data format="txt" name="output"/>
	</outputs>
	
	<help>

.. class:: infomark

**Purpose**

FastQC aims to provide a simple way to do some quality control checks on raw
sequence data coming from high throughput sequencing pipelines. 
It provides a modular set of analyses which you can use to give a quick
impression of whether your data has any problems of 
which you should be aware before doing any further analysis.

**FastQC documentation**

This is a Galaxy interface to the external package FastQC_.
Specific documentation on FastQC can be found on that site.

 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

-----

.. class:: infomark

**Inputs and outputs**

This wrapper will accept one or more fastq files.

The tool produces a single output file that contains summary of all the results, including the following:

- Basic Statistics
- Per base sequence quality
- Per sequence quality scores
- Per base sequence content
- Per base GC content
- Per sequence GC content
- Per base N content
- Sequence Length Distribution
- Sequence Duplication Levels
- Overrepresented sequences
- Kmer Content

	</help>
</tool>