Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/FastqIlluminaToSanger.xml @ 16:35031c567ece draft

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Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
author timpalpant
date Sat, 09 Jun 2012 16:06:25 -0400
parents 3e477c7e0e73
children
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1 <tool id="FastqIlluminaToSanger" name="Convert Fastq qualities" version="1.0.0">
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2 <description>from Illumina to Sanger</description>
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3 <command interpreter="sh">galaxyToolRunner.sh converters.FastqIlluminaToSanger -i $input -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="fastqillumina" label="FASTQ, Illumina qualities" />
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6 </inputs>
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7 <outputs>
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8 <data name="output" format="fastqsanger" metadata_source="input" />
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9 </outputs>
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10 <tests>
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11 <test>
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12 <param name="input" value="test.fastqillumina" ftype="fastqillumina"/>
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13 <output name="output" file="test.fastqsanger"/>
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14 </test>
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15 </tests>
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16 <help>
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18 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.
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20 For more information, read about FASTQ formats_ (right-click to open in new window).
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22 .. _formats: http://en.wikipedia.org/wiki/FASTQ_format
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24 .. class:: warningmark
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26 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.
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28 </help>
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29 </tool>