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1 <tool id="ctat_clean_headers" name="ctat_clean_headers" version="1.0.0" profile="17.05">
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2 <description>Clean read headers of fastq files</description>
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3 <requirements>
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4 <requirement type="package" version="5">perl</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 perl -lpe 'if (m/^[@+]/){ s/ //g}' "$input" > "$output"
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8 </command>
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9 <macros>
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10 </macros>
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11 <stdio>
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12 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
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13 </stdio>
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14 <regex match="Must investigate error above."
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15 source="stderr"
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16 level="fatal"
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17 description="Unknown error encountered" />
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18 <inputs>
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19 <param format="fastq" name="input" type="data" label="Fastq file with reads to be cleaned" help=""/>
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20 </inputs>
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21 <outputs>
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22 <data format="fastq" name="output" label="Cleaned ${on_string}" />
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23 </outputs>
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24 <tests>
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25 </tests>
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26 <help>
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27 Removes whitespace from the header of each read in a fastq file. If your Trinity run gives you errors with dying threads during the normalization step, try this tool on each input first.
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28 </help>
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29 <citations>
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30 </citations>
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31 </tool>
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