/tools/fastq/fastq_masker_by_quality.xml
https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 53 lines · 50 code · 3 blank · 0 comment · 0 complexity · 447e52a0843f35cf6fa505997f3cb391 MD5 · raw file
- <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0">
- <description>by quality score</description>
- <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}'
- #if $mask_type.value == 'lowercase'
- --lowercase
- #else
- -m '${mask_type}'
- #end if
- </command>
- <inputs>
- <param name="input_file" type="data" format="fastqsanger" label="File to mask" />
- <param name="mask_type" type="select" label="Mask input with">
- <option value="N">N's</option>
- <option value="lowercase">Lowercase</option>
- </param>
- <param name="score_comparison" type="select" label="When score is">
- <option value="le" selected="True">Less than or equal</option>
- <option value="lt">Less than</option>
- <option value="eq">Equal to</option>
- <option value="ne">Not Equal to</option>
- <option value="ge">Greater than</option>
- <option value="gt">Greater than or equal</option>
- </param>
- <param name="quality_score" type="integer" value="0"/>
- </inputs>
- <outputs>
- <data name="output_file" format="fastqsanger" />
- </outputs>
- <tests>
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="mask_type" value="N" />
- <param name="score_comparison" value="le" />
- <param name="quality_score" value="20" />
- <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" />
- </test>
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <param name="mask_type" value="lowercase" />
- <param name="score_comparison" value="le" />
- <param name="quality_score" value="20" />
- <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" />
- </test>
- </tests>
- <help>
- **What it does**
- This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method.
- This tool is not available for use on color space (csSanger) formats.
- </help>
- </tool>