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annotate fastq_trimmer.xml @ 2:fdff6f6a8763 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 19:31:05 -0500 |
| parents | 3be753901f6e |
| children | b849e7c23b43 |
| rev | line source |
|---|---|
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fdff6f6a8763
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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1 <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.1"> |
| 0 | 2 <description>by column</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">fastq_trimmer.py '$input_file' '$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'</command> | |
| 7 <inputs> | |
| 8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> | |
| 9 <conditional name="offset_type"> | |
| 10 <param name="base_offset_type" type="select" label="Define Base Offsets as" help="Use Absolute for fixed length reads (Illumina, SOLiD)<br>Use Percentage for variable length reads (Roche/454)"> | |
| 11 <option value="offsets_absolute" selected="true">Absolute Values</option> | |
| 12 <option value="offsets_percent">Percentage of Read Length</option> | |
| 13 </param> | |
| 14 <when value="offsets_absolute"> | |
| 15 <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> | |
| 16 <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> | |
| 17 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> | |
| 18 </param> | |
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2
fdff6f6a8763
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_trimmer commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
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19 <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" 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"> |
| 0 | 20 <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> |
| 21 </param> | |
| 22 </when> | |
| 23 <when value="offsets_percent"> | |
| 24 <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> | |
| 25 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> | |
| 26 </param> | |
| 27 <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> | |
| 28 <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> | |
| 29 </param> | |
| 30 </when> | |
| 31 </conditional> | |
| 32 <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="output_file" format="input" /> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <!-- Do nothing trim --> | |
| 40 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 41 <param name="base_offset_type" value="offsets_absolute"/> | |
| 42 <param name="left_column_offset" value="0"/> | |
| 43 <param name="right_column_offset" value="0"/> | |
| 44 <param name="keep_zero_length" value="keep_zero_length" /> | |
| 45 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> | |
| 46 </test> | |
| 47 <!-- Trim to empty File --> | |
| 48 <test> | |
| 49 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 50 <param name="base_offset_type" value="offsets_absolute"/> | |
| 51 <param name="left_column_offset" value="30"/> | |
| 52 <param name="right_column_offset" value="64"/> | |
| 53 <param name="keep_zero_length" value="exclude_zero_length" /> | |
| 54 <output name="output_file" file="empty_file.dat" /> | |
| 55 </test> | |
| 56 <test> | |
| 57 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 58 <param name="base_offset_type" value="offsets_percent"/> | |
| 59 <param name="left_column_offset" value="50"/> | |
| 60 <param name="right_column_offset" value="50"/> | |
| 61 <param name="keep_zero_length" value="exclude_zero_length" /> | |
| 62 <output name="output_file" file="empty_file.dat" /> | |
| 63 </test> | |
| 64 <!-- Trim to 4 inner-most bases --> | |
| 65 <test> | |
| 66 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 67 <param name="base_offset_type" value="offsets_absolute"/> | |
| 68 <param name="left_column_offset" value="45"/> | |
| 69 <param name="right_column_offset" value="45"/> | |
| 70 <param name="keep_zero_length" value="exclude_zero_length" /> | |
| 71 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> | |
| 72 </test> | |
| 73 <test> | |
| 74 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 75 <param name="base_offset_type" value="offsets_percent"/> | |
| 76 <param name="left_column_offset" value="47.87"/> | |
| 77 <param name="right_column_offset" value="47.87"/> | |
| 78 <param name="keep_zero_length" value="exclude_zero_length" /> | |
| 79 <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> | |
| 80 </test> | |
| 81 </tests> | |
| 82 <help> | |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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83 **What is does** |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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84 |
| 0 | 85 This tool allows you to trim the ends of reads. |
| 86 | |
| 87 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. | |
| 88 | |
| 89 For example, if you have a read of length 36:: | |
| 90 | |
| 91 @Some FASTQ Sanger Read | |
| 92 CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA | |
| 93 + | |
| 94 =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ | |
| 95 | |
| 96 And you set absolute offsets of 2 and 9:: | |
| 97 | |
| 98 @Some FASTQ Sanger Read | |
| 99 ATATGTNCTCACTGATAAGTGGATA | |
| 100 + | |
| 101 @.@;B-%?8>CBA@>7@7BBCA4-4 | |
| 102 | |
| 103 Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: | |
| 104 | |
| 105 @Some FASTQ Sanger Read | |
| 106 ATATGTNCTCACTGATAAGTGGATATN | |
| 107 + | |
| 108 @.@;B-%?8>CBA@>7@7BBCA4-48% | |
| 109 | |
| 110 ----- | |
| 111 | |
| 112 .. class:: warningmark | |
| 113 | |
| 114 Trimming a color space read will cause any adapter base to be lost. | |
| 115 | |
| 116 ------ | |
| 117 | |
| 118 </help> | |
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119 |
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120 <citations> |
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121 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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122 </citations> |
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123 |
| 0 | 124 </tool> |