[2] | 1 | <tool id="Sff_extractor" name="SFF converter" version="1.0.0"> |
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| 2 | <description></description> |
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| 3 | <command interpreter="python"> |
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| 4 | #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input |
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| 5 | #elif str($fastq_output) == "fastq_true" #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input |
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| 6 | #end if# |
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| 7 | </command> |
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| 8 | <inputs> |
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| 9 | <param format="sff" name="input" type="data" label="Extract from this dataset"/> |
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| 10 | <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence"> |
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| 11 | <option value="">No</option> |
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| 12 | <option value="--clip">Yes</option> |
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| 13 | </param> |
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| 14 | <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?" /> |
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| 15 | </inputs> |
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| 16 | <outputs> |
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| 17 | <data format="fastqsanger" name="out_file1" > |
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| 18 | <filter>fastq_output is True</filter> |
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| 19 | </data> |
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| 20 | <data format="xml" name="out_file2"> |
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| 21 | </data> |
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| 22 | <data format="fasta" name="out_file3"> |
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| 23 | <filter>fastq_output is False</filter> |
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| 24 | </data> |
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| 25 | <data format="qual" name="out_file4"> |
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| 26 | <filter>fastq_output is False</filter> |
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| 27 | </data> |
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| 28 | </outputs> |
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| 29 | <tests> |
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| 30 | <test> |
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| 31 | <param name="input" value="2.sff"/> |
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| 32 | <param name="clip" value=""/> |
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| 33 | <param name="fastq_output" value="false"/> |
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| 34 | <output name="out_file2" file="sff_converter_xml_1.dat"/> |
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| 35 | <output name="out_file3" file="sff_converter_fasta.dat"/> |
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| 36 | <output name="out_file4" file="sff_converter_qual.dat"/> |
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| 37 | </test> |
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| 38 | <test> |
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| 39 | <param name="input" value="2.sff"/> |
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| 40 | <param name="clip" value=""/> |
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| 41 | <param name="fastq_output" value="true"/> |
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| 42 | <output name="out_file1" file="sff_converter_fastq.dat"/> |
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| 43 | <output name="out_file2" file="sff_converter_xml_2.dat"/> |
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| 44 | </test> |
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| 45 | </tests> |
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| 46 | <help> |
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| 47 | |
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| 48 | **What it does** |
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| 49 | |
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| 50 | This tool extracts data from the 454 Sequencer SFF format and creates three files containing the: |
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| 51 | Sequences (FASTA), |
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| 52 | Qualities (QUAL) and |
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| 53 | Clippings (XML) |
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| 54 | |
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| 55 | </help> |
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| 56 | </tool> |
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| 57 | |
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| 58 | |
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