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1 <?xml version="1.0"?>
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2 <tool id="gbtofasta" name="gbToFasta" version="1.0">
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3 <description>Convert GenBank records to fasta and Create table with coding regions information for each mRNA record</description>
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4 <requirements>
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5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 gbToFaRa
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9 /dev/null
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10 '${outputfa}'
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11 outputra
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12 outputta
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13 '${gbfile}'
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14 #if $cds == "yes"
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15 && raToTab
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16 -cols=acc,cds
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17 outputra
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18 '${outputcds}'
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19 #end if
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20 ]]></command>
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21 <inputs>
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22 <param type="data" name="gbfile" format="genbank" />
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23 <param type="select" name="cds" label="Create table with coding regions information for each mRNA record" >
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24 <option value="yes">Yes</option>
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25 <option value="no">No</option>
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26 </param>
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27
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28 </inputs>
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29 <outputs>
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30 <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data>
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31 <data format="fasta" name="outputcds" label="${tool.name} on ${on_string}:cds">
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32 <filter>cds == "yes"</filter>
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
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38 <param name="cds" value="yes" />
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39 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
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40 <output name="outputcds" value="Gallus_gallus_RefSeq.cds" />
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41 </test>
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42 <test>
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43 <param name="gbfile" value="Gallus_gallus_RefSeq.gb" />
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44 <param name="cds" value="no" />
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45 <output name="outputfa" value="Gallus_gallus_RefSeq.fa" />
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46 </test>
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47 </tests>
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48 <help>
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49 <![CDATA[
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50 gbToFasta
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51 =========
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52
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53 Convert GenBank records to fasta
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54 ---------------------------------
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55
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56 gbToFaRa - Convert GenBank flat format file to an fa file containing
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57 the sequence data, an ra file containing other relevant info and
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58 a ta file containing summary statistics.
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59 usage:
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60 gbToFaRa filterFile faFile raFile taFile genBankFile(s)
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61 where filterFile is definition of which records and fields
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62 use /dev/null if you want no filtering.
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63
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64 gbToFaRa /dev/null gbfile.fa \
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65 gbfile.ra gbfile.ta gbfile
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66
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67 Create table with coding regions information for each mRNA record
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68 -----------------------------------------------------------------
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69 raToTab - Convert ra file to table.
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70 raToTab -cols=acc,cds gbfile.ra gbfile.cds
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71
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72 Source code:
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73 ============
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74
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75 http://hgdownload.cse.ucsc.edu/admin/exe/
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76
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77 ]]></help>
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78 <citations>
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79 <citation type="bibtex">@article{kent2002blat,
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80 title={BLAT—the BLAST-like alignment tool},
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81 author={Kent, W James},
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82 journal={Genome research},
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83 volume={12},
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84 number={4},
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85 pages={656--664},
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86 year={2002},
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87 publisher={Cold Spring Harbor Lab}
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88 }</citation>
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89 </citations>
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90
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91 </tool>
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