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