Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/FastqIlluminaToSanger.xml @ 15:3e477c7e0e73 draft

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Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents eb53be9a09f4
children
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--- a/galaxy-conf/FastqIlluminaToSanger.xml	Sat May 19 10:40:16 2012 -0400
+++ b/galaxy-conf/FastqIlluminaToSanger.xml	Sat Jun 09 16:03:59 2012 -0400
@@ -15,11 +15,15 @@
   </tests>
 <help>
 
-This tool will convert a FASTQ file with ASCII quality scores encoded in Illumina 1.3 format (Phred+64) to Sanger format (Phred+33). It is a simpler, faster version of the FASTQ Groomer.
+This tool will convert a FASTQ file with ASCII quality scores encoded in Illumina 1.3-1.7 format (Phred+64) to Sanger format (Phred+33) for use with Bowtie and other Galaxy tools. Illumina CASAVA >= 1.8 already produces FASTQ files in Sanger format, so this tool should not be used on new Illumina sequencing data. This tool is a simpler, faster version of the FASTQ Groomer that does little error checking but performs much faster. If you are unsure what format your file is in, or need to do other conversions, use the FASTQ Groomer instead.
+
+For more information, read about FASTQ formats_ (right-click to open in new window).
+
+.. _formats: http://en.wikipedia.org/wiki/FASTQ_format
 
 .. class:: warningmark
 	
-This tool requires fastqillumina formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
+This tool requires fastqillumina formatted data. If you have fastq data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
 
 </help>
 </tool>