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annotate removeLowQualityBases.xml @ 0:0475e4175855 draft default tip

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author yqiancolumbia
date Mon, 30 Apr 2018 05:25:11 -0400
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1 <tool id="removeLowQualityBases" name="Remove low quality bases">
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2 <description></description>
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3
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4 <command>
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5 fastq_quality_trimmer -i $input -v -l $MinimumLength $CompressOutput -t $Qualitythreshold -o $output
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6 </command>
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7
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8 <inputs>
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9 <param name="input" type="data" format="fastq" label="Input FASTQ file"/>
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10 <param name="Qualitythreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/>
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11 <param name="MinimumLength" type="integer" value="29" label="Minimum length - sequences shorter than this (after trimming) will be discarded (0 = no minimum length)"/>
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12 <param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/>
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13 </inputs>
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14
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15 <outputs>
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16 <data name="output" format="fastq" />
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17 </outputs>
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18 <help>
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19
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20 .. class:: infomark
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21
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22 **What this tool does**
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23
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24 This tool (fastq_quality_trimmer) will remove extremely low quality bases (e.g. score less than 5).
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25
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26 It will take as input FASTQ files and output FASTQ files with low quality bases removed.
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27
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28 It is a part of the Fastx Toolkit.
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29
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30 -----
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31
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32 **Parameter suggestion for minimum length**
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33
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34 * For standard CLIP: discard sequences shorter than 20 nucleotides.
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35 * For BrdU CLIP: discard sequences shorter than 29 nucleotides.
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36
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37 </help>
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38
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39 </tool>