/tools/fastq/fastq_trimmer.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 120 lines · 102 code · 15 blank · 3 comment · 0 complexity · 9c7ca9155c769e08e2948bbe8cfcf190 MD5 · raw file
- <tool id="fastq_trimmer" name="FASTQ Trimmer" version="1.0.0">
- <description>by column</description>
- <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>
- <inputs>
- <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ File"/>
- <conditional name="offset_type">
- <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)">
- <option value="offsets_absolute" selected="true">Absolute Values</option>
- <option value="offsets_percent">Percentage of Read Length</option>
- </param>
- <when value="offsets_absolute">
- <param name="left_column_offset" label="Offset from 5' end" value="0" type="integer" help="Values start at 0, increasing from the left">
- <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
- <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
- </param>
- <param name="right_column_offset" label="Offset from 3' end" value="0" type="integer" help="Values start at 0, increasing from the right">
- <validator type="in_range" message="Base Offsets must be positive" min="0" max="inf"/>
- <validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
- </param>
- </when>
- <when value="offsets_percent">
- <param name="left_column_offset" label="Offset from 5' end" value="0" type="float">
- <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>
- </param>
- <param name="right_column_offset" label="Offset from 3' end" value="0" type="float">
- <validator type="in_range" message="Base Offsets must be between 0 and 100" min="0" max="100"/>
- </param>
- </when>
- </conditional>
- <param name="keep_zero_length" label="Keep reads with zero length" type="boolean" truevalue="keep_zero_length" falsevalue="exclude_zero_length" selected="False"/>
- </inputs>
- <outputs>
- <data name="output_file" format="input" />
- </outputs>
- <tests>
- <test>
- <!-- Do nothing trim -->
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="base_offset_type" value="offsets_absolute"/>
- <param name="left_column_offset" value="0"/>
- <param name="right_column_offset" value="0"/>
- <param name="keep_zero_length" value="keep_zero_length" />
- <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
- </test>
- <!-- Trim to empty File -->
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="base_offset_type" value="offsets_absolute"/>
- <param name="left_column_offset" value="30"/>
- <param name="right_column_offset" value="64"/>
- <param name="keep_zero_length" value="exclude_zero_length" />
- <output name="output_file" file="empty_file.dat" />
- </test>
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="base_offset_type" value="offsets_percent"/>
- <param name="left_column_offset" value="50"/>
- <param name="right_column_offset" value="50"/>
- <param name="keep_zero_length" value="exclude_zero_length" />
- <output name="output_file" file="empty_file.dat" />
- </test>
- <!-- Trim to 4 inner-most bases -->
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="base_offset_type" value="offsets_absolute"/>
- <param name="left_column_offset" value="45"/>
- <param name="right_column_offset" value="45"/>
- <param name="keep_zero_length" value="exclude_zero_length" />
- <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
- </test>
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="base_offset_type" value="offsets_percent"/>
- <param name="left_column_offset" value="47.87"/>
- <param name="right_column_offset" value="47.87"/>
- <param name="keep_zero_length" value="exclude_zero_length" />
- <output name="output_file" file="fastq_trimmer_out1.fastqsanger" />
- </test>
- </tests>
- <help>
- This tool allows you to trim the ends of reads.
- 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.
- For example, if you have a read of length 36::
-
- @Some FASTQ Sanger Read
- CAATATGTNCTCACTGATAAGTGGATATNAGCNCCA
- +
- =@@.@;B-%?8>CBA@>7@7BBCA4-48%<;;%<B@
-
- And you set absolute offsets of 2 and 9::
-
- @Some FASTQ Sanger Read
- ATATGTNCTCACTGATAAGTGGATA
- +
- @.@;B-%?8>CBA@>7@7BBCA4-4
-
- Or you set percent offsets of 6% and 20% (corresponds to absolute offsets of 2,7 for a read length of 36)::
-
- @Some FASTQ Sanger Read
- ATATGTNCTCACTGATAAGTGGATATN
- +
- @.@;B-%?8>CBA@>7@7BBCA4-48%
-
- -----
- .. class:: warningmark
- Trimming a color space read will cause any adapter base to be lost.
- ------
- **Citation**
- If 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>`_
- </help>
- </tool>