/tools/filters/sff_extractor.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 58 lines · 53 code · 5 blank · 0 comment · 0 complexity · 688a504efe92059b62cc226848fbf9eb MD5 · raw file
- <tool id="Sff_extractor" name="SFF converter" version="1.0.1">
- <description></description>
- <command interpreter="python">
- #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
- #elif str($fastq_output) == "fastq_true" #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input
- #end if#
- </command>
- <inputs>
- <param format="sff" name="input" type="data" label="Extract from this dataset"/>
- <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
- <option value="">No</option>
- <option value="--clip">Yes</option>
- </param>
- <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" />
- </inputs>
- <outputs>
- <data format="fastqsanger" name="out_file1" >
- <filter>fastq_output is True</filter>
- </data>
- <data format="xml" name="out_file2">
- </data>
- <data format="fasta" name="out_file3">
- <filter>fastq_output is False</filter>
- </data>
- <data format="qual" name="out_file4">
- <filter>fastq_output is False</filter>
- </data>
- </outputs>
- <tests>
- <test>
- <param name="input" value="2.sff"/>
- <param name="clip" value=""/>
- <param name="fastq_output" value="false"/>
- <output name="out_file2" file="sff_converter_xml_1.dat"/>
- <output name="out_file3" file="sff_converter_fasta.dat"/>
- <output name="out_file4" file="sff_converter_qual.dat"/>
- </test>
- <test>
- <param name="input" value="2.sff"/>
- <param name="clip" value=""/>
- <param name="fastq_output" value="true"/>
- <output name="out_file1" file="sff_converter_fastq.dat"/>
- <output name="out_file2" file="sff_converter_xml_2.dat"/>
- </test>
- </tests>
- <help>
- **What it does**
- This tool extracts data from the 454 Sequencer SFF format and creates three files containing the:
- Sequences (FASTA),
- Qualities (QUAL) and
- Clippings (XML)
- </help>
- </tool>