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annotate 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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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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3e477c7e0e73 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.
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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.
3e477c7e0e73 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.
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3e477c7e0e73 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.
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20 For more information, read about FASTQ formats_ (right-click to open in new window).
3e477c7e0e73 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.
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3e477c7e0e73 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.
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22 .. _formats: http://en.wikipedia.org/wiki/FASTQ_format
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24 .. class:: warningmark
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3e477c7e0e73 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.
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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>