[2] | 1 | <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0"> |
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| 2 | <description>by quality score</description> |
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| 3 | <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}' |
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| 4 | #if $mask_type.value == 'lowercase' |
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| 5 | --lowercase |
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| 6 | #else |
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| 7 | -m '${mask_type}' |
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| 8 | #end if |
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| 9 | </command> |
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| 10 | <inputs> |
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| 11 | <param name="input_file" type="data" format="fastqsanger" label="File to mask" /> |
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| 12 | <param name="mask_type" type="select" label="Mask input with"> |
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| 13 | <option value="N">N's</option> |
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| 14 | <option value="lowercase">Lowercase</option> |
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| 15 | </param> |
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| 16 | <param name="score_comparison" type="select" label="When score is"> |
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| 17 | <option value="le" selected="True">Less than or equal</option> |
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| 18 | <option value="lt">Less than</option> |
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| 19 | <option value="eq">Equal to</option> |
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| 20 | <option value="ne">Not Equal to</option> |
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| 21 | <option value="ge">Greater than</option> |
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| 22 | <option value="gt">Greater than or equal</option> |
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| 23 | </param> |
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| 24 | <param name="quality_score" type="integer" value="0"/> |
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| 25 | </inputs> |
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| 26 | <outputs> |
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| 27 | <data name="output_file" format="fastqsanger" /> |
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| 28 | </outputs> |
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| 29 | <tests> |
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| 30 | <test> |
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| 31 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
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| 32 | <param name="mask_type" value="N" /> |
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| 33 | <param name="score_comparison" value="le" /> |
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| 34 | <param name="quality_score" value="20" /> |
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| 35 | <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" /> |
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| 36 | </test> |
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| 37 | <test> |
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| 38 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
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| 39 | <param name="mask_type" value="lowercase" /> |
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| 40 | <param name="score_comparison" value="le" /> |
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| 41 | <param name="quality_score" value="20" /> |
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| 42 | <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" /> |
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| 43 | </test> |
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| 44 | </tests> |
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| 45 | <help> |
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| 46 | **What it does** |
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| 47 | |
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| 48 | This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method. |
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| 49 | |
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| 50 | This tool is not available for use on color space (csSanger) formats. |
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| 51 | |
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| 52 | </help> |
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| 53 | </tool> |
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