/tools/filters/sff_extractor.xml

 1<tool id="Sff_extractor" name="SFF converter" version="1.0.1">
 2    <description></description>
 3    <command interpreter="python">
 4        #if   str($fastq_output) == "fastq_false"  #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
 5        #elif str($fastq_output) == "fastq_true"   #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input
 6        #end if#
 7    </command>
 8    <inputs>
 9        <param format="sff" name="input" type="data" label="Extract from this dataset"/>
10        <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
11            <option value="">No</option>
12            <option value="--clip">Yes</option>
13        </param>
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?" />
15    </inputs>
16    <outputs>
17        <data format="fastqsanger" name="out_file1" >
18            <filter>fastq_output is True</filter>
19        </data>
20        <data format="xml" name="out_file2">
21        </data>  
22        <data format="fasta" name="out_file3">
23            <filter>fastq_output is False</filter>
24        </data>
25        <data format="qual" name="out_file4">
26            <filter>fastq_output is False</filter>
27        </data>
28    </outputs>
29    <tests>
30        <test>
31            <param name="input" value="2.sff"/>
32            <param name="clip" value=""/>
33            <param name="fastq_output" value="false"/>
34            <output name="out_file2" file="sff_converter_xml_1.dat"/>
35            <output name="out_file3" file="sff_converter_fasta.dat"/>
36            <output name="out_file4" file="sff_converter_qual.dat"/>
37        </test>
38        <test>
39            <param name="input" value="2.sff"/>
40            <param name="clip" value=""/>
41            <param name="fastq_output" value="true"/>
42            <output name="out_file1" file="sff_converter_fastq.dat"/>
43            <output name="out_file2" file="sff_converter_xml_2.dat"/>
44        </test>
45    </tests>
46    <help>
47
48**What it does**
49
50This tool extracts data from the 454 Sequencer SFF format and creates three files containing the: 
51Sequences (FASTA),
52Qualities (QUAL) and 
53Clippings (XML)
54
55    </help>
56</tool>
57
58