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1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
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7 <inputs>
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8 <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
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9 </inputs>
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10 <outputs>
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11 <data name="output_file" format="fasta" />
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12 </outputs>
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13 <tests>
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14 <!-- basic test -->
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15 <test>
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16 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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17 <output name="output_file" file="fastq_to_fasta_python_1.out" />
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18 </test>
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19 <!-- color space test -->
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20 <test>
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21 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
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22 <output name="output_file" file="fastq_to_fasta_python_2.out" />
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23 </test>
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24 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
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25 <test>
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26 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
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27 <output name="output_file" file="fastq_to_fasta_python_1.out" />
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28 </test>
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29 </tests>
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30 <help>
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31 **What it does**
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32
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33 This tool converts FASTQ sequencing reads to FASTA sequences.
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34
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35 ------
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36
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37 **Citation**
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38
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39 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_
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40
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41
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42 </help>
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43 </tool>
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