Mercurial > repos > devteam > fastq_trimmer_by_quality

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 12:23:48 +0000
parents 8b85db5a62e6
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de3d8685fe42 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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1 <tool id="fastq_quality_trimmer" name="FASTQ Quality Trimmer" version="1.1.5" profile="16.04">
4
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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2 <description>by sliding window</description>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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3 <requirements>
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de3d8685fe42 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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4 <requirement type="package" version="1.1.5">galaxy_sequence_utils</requirement>
4
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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6 <command><![CDATA[
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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7 gx-fastq-trimmer-by-quality '$input_file' '$output_file' -f '${input_file.extension[len('fastq'):]}' -s $window_size
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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8 -t $step_size -e $trim_ends -a $aggregation_action -x $exclude_count -c '$score_comparison' -q $quality_score
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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9 #if $keep_zero_length:
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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10 -k
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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11 #end if
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12 ]]></command>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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13 <inputs>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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14 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="FASTQ File"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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15 <param name="keep_zero_length" type="boolean" checked="false" label="Keep reads with zero length"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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16 <param name="trim_ends" type="select" label="Trim ends">
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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17 <option value="53" selected="true">5' and 3'</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 <option value="5">5' only</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 <option value="3">3' only</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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20 </param>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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21 <param name="window_size" type="integer" value="1" label="Window size"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 <param name="step_size" type="integer" value="1" label="Step size" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 <param name="exclude_count" type="integer" value="0" label="Maximum number of bases to exclude from the window during aggregation" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <param name="aggregation_action" type="select" label="Aggregate action for window">
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 <option value="min" selected="true">min score</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 <option value="max">max score</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 <option value="sum">sum of scores</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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28 <option value="mean">mean of scores</option>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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29 </param>
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30 <param name="score_comparison" type="select" label="Trim until aggregate score is">
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31 <sanitizer>
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32 <valid initial="none">
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33 <add value="&lt;&gt;=!"/> <!-- only allow lt, gt, e, le, ge, ne for this parameter; will be single-quote escaped on commandline -->
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 </valid>
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35 </sanitizer>
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36 <option value="&gt;">&gt;</option>
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37 <option value="&gt;=" selected="true">&gt;=</option>
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38 <option value="==">==</option>
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39 <option value="!=">!=</option>
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40 <option value="&lt;">&lt;</option>
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41 <option value="&lt;=">&lt;=</option>
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42 </param>
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43 <param name="quality_score" type="float" value="0" label="Quality score" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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44 </inputs>
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45 <outputs>
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46 <data name="output_file" format_source="input_file" />
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47 </outputs>
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48 <tests>
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49 <!-- Trim until window size 1 >= 20;both ends -->
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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50 <test>
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51 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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52 <param name="keep_zero_length" value="false" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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53 <param name="trim_ends" value="53"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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54 <param name="window_size" value="1"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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55 <param name="step_size" value="1"/>
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56 <param name="exclude_count" value="0"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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57 <param name="aggregation_action" value="min"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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58 <param name="score_comparison" value="&gt;="/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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59 <param name="quality_score" value="20"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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60 <output name="output_file" file="sanger_full_range_quality_trimmed_out_1.fastqsanger" ftype="fastqsanger" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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61 </test>
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62 <!-- Trim until window size 1 >= 20; 5' end only -->
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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63 <test>
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64 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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65 <param name="keep_zero_length" value="false" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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66 <param name="trim_ends" value="5"/>
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67 <param name="window_size" value="1"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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68 <param name="step_size" value="1"/>
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69 <param name="exclude_count" value="0"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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70 <param name="aggregation_action" value="min"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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71 <param name="score_comparison" value="&gt;="/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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72 <param name="quality_score" value="20"/>
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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73 <output name="output_file" file="sanger_full_range_quality_trimmed_out_2.fastqsanger" ftype="fastqsanger" />
8b85db5a62e6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality commit f2582539542b33240234e8ea6093e25d0aee9b6a
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74 </test>
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75 <!-- Trim until window size 1 >= 20; 3' end only -->
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76 <test>
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77 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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78 <param name="keep_zero_length" value="false" />
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79 <param name="trim_ends" value="3"/>
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80 <param name="window_size" value="1"/>
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81 <param name="step_size" value="1"/>
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82 <param name="exclude_count" value="0"/>
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83 <param name="aggregation_action" value="min"/>
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84 <param name="score_comparison" value="&gt;="/>
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85 <param name="quality_score" value="20"/>
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86 <output name="output_file" file="sanger_full_range_quality_trimmed_out_3.fastqsanger" ftype="fastqsanger" />
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87 </test>
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88 <!-- Trim until window size 2 >= 1;both ends, 1 deviant score -->
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89 <test>
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90 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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91 <param name="keep_zero_length" value="false" />
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92 <param name="trim_ends" value="53"/>
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93 <param name="window_size" value="2"/>
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94 <param name="step_size" value="1"/>
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95 <param name="exclude_count" value="1"/>
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96 <param name="aggregation_action" value="min"/>
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97 <param name="score_comparison" value="&gt;="/>
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98 <param name="quality_score" value="1"/>
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99 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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100 </test>
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101 <!-- Trim entire sequences; keep empty reads -->
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102 <test>
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103 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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104 <param name="keep_zero_length" value="true" />
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105 <param name="trim_ends" value="53"/>
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106 <param name="window_size" value="1"/>
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107 <param name="step_size" value="1"/>
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108 <param name="exclude_count" value="0"/>
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109 <param name="aggregation_action" value="min"/>
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110 <param name="score_comparison" value="&gt;="/>
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111 <param name="quality_score" value="999"/>
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112 <output name="output_file" file="sanger_full_range_empty_reads.fastqsanger" ftype="fastqsanger" />
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113 </test>
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114 <!-- Trim entire sequences; discard empty reads -->
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115 <test>
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116 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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117 <param name="keep_zero_length" value="false" />
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118 <param name="trim_ends" value="53"/>
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119 <param name="window_size" value="1"/>
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120 <param name="step_size" value="1"/>
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121 <param name="exclude_count" value="0"/>
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122 <param name="aggregation_action" value="min"/>
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123 <param name="score_comparison" value="&gt;="/>
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124 <param name="quality_score" value="999"/>
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125 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
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126 </test>
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127 </tests>
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128 <help><![CDATA[
1
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129 **What it does**
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130
3
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131 This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.
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132
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133 The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found within the sliding window to be used with the user defined comparison operation and comparison value.
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134
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135 The user can provide a maximum count of bases that can be excluded from the aggregation within the window. When set, this tool will first check the aggregation of the entire window, then after removing 1 value, then after removing 2 values, up to the number declared. Setting this value to be equal to or greater than the window size will cause no trimming to occur.
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136
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137 -----
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138
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139 .. class:: warningmark
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140
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141 Trimming a color space read will cause any adapter base to be lost.
4
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142 ]]></help>
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143 <citations>
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144 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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145 </citations>
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146 </tool>