diff fastqc_checker.xml @ 0:d8d131d08779 draft default tip

Initial upload.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_checker.xml	Tue May 21 11:48:53 2013 -0400
@@ -0,0 +1,57 @@
+<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>