Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/FastqIlluminaToSanger.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
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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="bash">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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17
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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>