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comparison sffextract.xml @ 1:dc29406ce984 draft

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author biowebdb
date Mon, 31 Mar 2014 14:10:35 -0400
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1 <tool id="biowebdb_flowgram_sffextract" name="sffextract" version="1.0.0">
2 <description>Convert SFF to FastQ or Fasta/Qual</description>
3 <requirements>
4 <requirement type="binary">sff_extract</requirement>
5 </requirements>
6 <command interpreter="ruby">sffextract.rb
7 $input
8 #if str( $format_options.format ) == "FASTQ"
9 $output1
10 #else
11 $output2 $output3
12 #end if
13 </command>
14 <inputs>
15 <param name="input" type="data" format="sff" label="Input from 454 (flowgram - sff)" help="Only SFF file"/>
16 <conditional name="format_options">
17 <param name="format" type="select" label="Output format" help="">
18 <option value="FASTQ" selected="true">FastQ</option>
19 <option value="FASTA">Fasta</option>
20 </param>
21 </conditional>
22 </inputs>
23 <outputs>
24 <data name="output1" format="fastq" label="FASTQ - ${tool.name} on ${input.name}">
25 <filter>format_options['format'] == 'FASTQ'</filter>
26 </data>
27 <data name="output2" format="fasta" label="FASTA - ${tool.name} on ${input.name}">
28 <filter>format_options['format'] == 'FASTA'</filter>
29 </data>
30 <data name="output3" format="qual" label="QUAL - ${tool.name} on ${input.name}">
31 <filter>format_options['format'] == 'FASTA'</filter>
32 </data>
33 </outputs>
34 <stdio>
35 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
36 <exit_code range="1:" level="fatal"/>
37 </stdio>
38 <tests>
39 <test>
40 <!--
41 <param name="input" value="file454.sff"/>
42 <param name="format" value="FASTQ"/>
43 <output name="outfile1" file="file454.sff.fastq"/>
44 <output name="outfile1" file="file454.sff.fasta"/>
45 <output name="outfile2" file="file454.sff.qual"/>
46 -->
47 </test>
48 </tests>
49 <help>
50
51 **If you use this tool, please cite:**
52
53 | `Wagner G`_, Jardim R, Tschoeke DA, Loureiro DR, Ocana KACS, Ribeiro ACB, Emmel VE,
54 | Probst CM, Pitaluga AN, Grisard EC, Cavalcanti MC, Campos MLM, Mattoso M and `Dávila AMR`_
55 | **STINGRAY: system for integrated genomic resources and analysis**
56 | BMC Research Notes 2014, 7:132
57
58 .. _Wagner G: glauber@ccb.ufsc.br
59 .. _Dávila AMR: davila@ioc.fiocruz.br
60
61 -----
62
63 If you have any questions or comments, feel free to `contact us`_.
64
65 .. _contact us: jardim@ioc.fiocruz.br
66
67 -----
68
69 **Sff_extract information**
70
71 454 sequence reads are usually stored in sff files. In these files the information about the reads is stored: sequece, quality and quality and adapter clips. sff_extract extracts the reads from the sff files and stores them into fasta and xml or caf text files.
72 sff_extract is a command line application written in python and it's free software distributed under the GPL licence. This software has been coded by Jose Blanca and Bastien Chevreux. See http://bioinf.comav.upv.es/sff_extract/index.html"
73 </help>
74
75 </tool>