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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" label="Quality score"/>
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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 ------
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53
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54 **Citation**
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55
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56 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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57
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58
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59 </help>
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60 </tool>
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