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annotate fastq_trimmer.xml @ 2:430b9da91435 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 13:55:56 -0400
parents e0cfb5a703ce
children 2d0d13b0b0f1
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430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.1.1">
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2 <description>by column</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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5 </requirements>
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6 <command><![CDATA[
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7 gx-fastq-trimmer '$input_file' '$output_file' ${offset_type['left_column_offset']} ${offset_type['right_column_offset']} ${offset_type['base_offset_type']} '${input_file.extension[len('fastq'):]}' $keep_zero_length
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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8 ]]></command>
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9 <inputs>
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10 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz" label="FASTQ file"/>
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11 <conditional name="offset_type">
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12 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)&lt;br&gt;Use Percentage for variable length reads (Roche/454)">
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13 <option value="offsets_absolute" selected="true">Absolute Values</option>
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14 <option value="offsets_percent">Percentage of Read Length</option>
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15 </param>
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16 <when value="offsets_absolute">
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17 <param name="left_column_offset" type="integer" min="0" value="0" label="Offset from 5' end" help="Values start at 0, increasing from the left" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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18 <param name="right_column_offset" type="integer" value="0" label="Offset from 3' end" help="Values start at 0, increasing from the right; use a negative value to remove everything to the right of the absolute value of the position" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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19 </when>
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20 <when value="offsets_percent">
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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21 <param name="left_column_offset" type="float" min="0" max="100" value="0" label="Offset from 5' end" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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22 <param name="right_column_offset" type="float" min="0" max="100" value="0" label="Offset from 3' end" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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23 </when>
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24 </conditional>
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25 <param name="keep_zero_length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" checked="false" label="Keep reads with zero length" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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26 </inputs>
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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27 <outputs>
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28 <data name="output_file" format_source="input_file" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <!-- Do nothing trim -->
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33 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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34 <param name="base_offset_type" value="offsets_absolute"/>
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35 <param name="left_column_offset" value="0"/>
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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36 <param name="right_column_offset" value="0"/>
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37 <param name="keep_zero_length" value="keep_zero_length" />
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38 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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39 </test>
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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40 <!-- Trim to empty File -->
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41 <test>
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42 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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43 <param name="base_offset_type" value="offsets_absolute"/>
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44 <param name="left_column_offset" value="30"/>
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45 <param name="right_column_offset" value="64"/>
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46 <param name="keep_zero_length" value="exclude_zero_length" />
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47 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
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48 </test>
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49 <test>
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50 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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51 <param name="base_offset_type" value="offsets_percent"/>
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52 <param name="left_column_offset" value="50"/>
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53 <param name="right_column_offset" value="50"/>
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54 <param name="keep_zero_length" value="exclude_zero_length" />
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55 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
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56 </test>
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57 <!-- Trim to 4 inner-most bases -->
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58 <test>
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59 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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60 <param name="base_offset_type" value="offsets_absolute"/>
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61 <param name="left_column_offset" value="45"/>
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62 <param name="right_column_offset" value="45"/>
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63 <param name="keep_zero_length" value="exclude_zero_length" />
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64 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
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65 </test>
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66 <test>
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67 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
430b9da91435 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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68 <param name="base_offset_type" value="offsets_percent"/>
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69 <param name="left_column_offset" value="47.87"/>
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70 <param name="right_column_offset" value="47.87"/>
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71 <param name="keep_zero_length" value="exclude_zero_length" />
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72 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" ftype="fastqsanger" />
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73 </test>
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74 </tests>
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75 <help><![CDATA[
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76 **What is does**
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77
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78 This tool allows you to trim the ends of reads.
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79
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80 You can specify either absolute or percent-based offsets. Offsets are calculated, starting at 0, from the respective end to be trimmed. When using the percent-based method, offsets are rounded to the nearest integer.
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81
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82 For example, if you have a read of length 36::
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83
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84 @Some FASTQ Sanger Read
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85 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
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86 +
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87 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@
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88
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89 And you set absolute offsets of 2 and 9::
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90
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91 @Some FASTQ Sanger Read
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92 ATATGTNCTCACTGATAAGTGGATA
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93 +
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94 @.@;B-%?8>CBA@>7@7BBCA4-4
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95
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96 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36)::
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97
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98 @Some FASTQ Sanger Read
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99 ATATGTNCTCACTGATAAGTGGATATN
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100 +
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101 @.@;B-%?8>CBA@>7@7BBCA4-48%
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102
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103 -----
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104
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105 .. class:: warningmark
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106
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107 Trimming a color space read will cause any adapter base to be lost.
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108 ]]></help>
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109 <citations>
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110 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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111 </citations>
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112 </tool>