Mercurial > repos > xuebing > sharplabtool
view tools/filters/sff_extractor.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="Sff_extractor" name="SFF converter" version="1.0.0"> <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>