/tools/fastq/fastq_trimmer.xml
XML | 120 lines | 102 code | 15 blank | 3 comment | 0 complexity | 9c7ca9155c769e08e2948bbe8cfcf190 MD5 | raw file
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> 81This tool allows you to trim the ends of reads. 82 83You 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 85For 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 92And 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 99Or 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 110Trimming a color space read will cause any adapter base to be lost. 111 112------ 113 114**Citation** 115 116If 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>`_ 117 118 119 </help> 120</tool>