[2] | 1 | <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0"> |
---|
| 2 | <description>by column</description> |
---|
| 3 | <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> |
---|
| 4 | <inputs> |
---|
| 5 | <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/> |
---|
| 6 | <conditional name="offset_type"> |
---|
| 7 | <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)"> |
---|
| 8 | <option value="offsets_absolute" selected="true">Absolute Values</option> |
---|
| 9 | <option value="offsets_percent">Percentage of Read Length</option> |
---|
| 10 | </param> |
---|
| 11 | <when value="offsets_absolute"> |
---|
| 12 | <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left"> |
---|
| 13 | <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> |
---|
| 14 | <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> |
---|
| 15 | </param> |
---|
| 16 | <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right"> |
---|
| 17 | <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/> |
---|
| 18 | <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator> |
---|
| 19 | </param> |
---|
| 20 | </when> |
---|
| 21 | <when value="offsets_percent"> |
---|
| 22 | <param name="left_column_offset" label="Offset from 5' end" value="0" type="float"> |
---|
| 23 | <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> |
---|
| 24 | </param> |
---|
| 25 | <param name="right_column_offset" label="Offset from 3' end" value="0" type="float"> |
---|
| 26 | <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/> |
---|
| 27 | </param> |
---|
| 28 | </when> |
---|
| 29 | </conditional> |
---|
| 30 | <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/> |
---|
| 31 | </inputs> |
---|
| 32 | <outputs> |
---|
| 33 | <data name="output_file" format="input" /> |
---|
| 34 | </outputs> |
---|
| 35 | <tests> |
---|
| 36 | <test> |
---|
| 37 | <!-- Do nothing trim --> |
---|
| 38 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 39 | <param name="base_offset_type" value="offsets_absolute"/> |
---|
| 40 | <param name="left_column_offset" value="0"/> |
---|
| 41 | <param name="right_column_offset" value="0"/> |
---|
| 42 | <param name="keep_zero_length" value="keep_zero_length" /> |
---|
| 43 | <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> |
---|
| 44 | </test> |
---|
| 45 | <!-- Trim to empty File --> |
---|
| 46 | <test> |
---|
| 47 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 48 | <param name="base_offset_type" value="offsets_absolute"/> |
---|
| 49 | <param name="left_column_offset" value="30"/> |
---|
| 50 | <param name="right_column_offset" value="64"/> |
---|
| 51 | <param name="keep_zero_length" value="exclude_zero_length" /> |
---|
| 52 | <output name="output_file" file="empty_file.dat" /> |
---|
| 53 | </test> |
---|
| 54 | <test> |
---|
| 55 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 56 | <param name="base_offset_type" value="offsets_percent"/> |
---|
| 57 | <param name="left_column_offset" value="50"/> |
---|
| 58 | <param name="right_column_offset" value="50"/> |
---|
| 59 | <param name="keep_zero_length" value="exclude_zero_length" /> |
---|
| 60 | <output name="output_file" file="empty_file.dat" /> |
---|
| 61 | </test> |
---|
| 62 | <!-- Trim to 4 inner-most bases --> |
---|
| 63 | <test> |
---|
| 64 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 65 | <param name="base_offset_type" value="offsets_absolute"/> |
---|
| 66 | <param name="left_column_offset" value="45"/> |
---|
| 67 | <param name="right_column_offset" value="45"/> |
---|
| 68 | <param name="keep_zero_length" value="exclude_zero_length" /> |
---|
| 69 | <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> |
---|
| 70 | </test> |
---|
| 71 | <test> |
---|
| 72 | <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> |
---|
| 73 | <param name="base_offset_type" value="offsets_percent"/> |
---|
| 74 | <param name="left_column_offset" value="47.87"/> |
---|
| 75 | <param name="right_column_offset" value="47.87"/> |
---|
| 76 | <param name="keep_zero_length" value="exclude_zero_length" /> |
---|
| 77 | <output name="output_file" file="fastq_trimmer_out1.fastqsanger" /> |
---|
| 78 | </test> |
---|
| 79 | </tests> |
---|
| 80 | <help> |
---|
| 81 | This tool allows you to trim the ends of reads. |
---|
| 82 | |
---|
| 83 | 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. |
---|
| 84 | |
---|
| 85 | For example, if you have a read of length 36:: |
---|
| 86 | |
---|
| 87 | @Some FASTQ Sanger Read |
---|
| 88 | CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA |
---|
| 89 | + |
---|
| 90 | =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@ |
---|
| 91 | |
---|
| 92 | And you set absolute offsets of 2 and 9:: |
---|
| 93 | |
---|
| 94 | @Some FASTQ Sanger Read |
---|
| 95 | ATATGTNCTCACTGATAAGTGGATA |
---|
| 96 | + |
---|
| 97 | @.@;B-%?8>CBA@>7@7BBCA4-4 |
---|
| 98 | |
---|
| 99 | Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36):: |
---|
| 100 | |
---|
| 101 | @Some FASTQ Sanger Read |
---|
| 102 | ATATGTNCTCACTGATAAGTGGATATN |
---|
| 103 | + |
---|
| 104 | @.@;B-%?8>CBA@>7@7BBCA4-48% |
---|
| 105 | |
---|
| 106 | ----- |
---|
| 107 | |
---|
| 108 | .. class:: warningmark |
---|
| 109 | |
---|
| 110 | Trimming a color space read will cause any adapter base to be lost. |
---|
| 111 | |
---|
| 112 | </help> |
---|
| 113 | </tool> |
---|