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annotate emboss_checktrans.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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1 <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0">
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2 <description>Reports STOP codons and ORF statistics of a protein</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>On query</label>
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8 </param>
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9 <param name="orfml" type="text" value="100">
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10 <label>Minimum ORF Length to report</label>
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11 </param>
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12 <param name="addlast" type="select">
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13 <label>An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there
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14 is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs</label>
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15 <option value="yes">Yes</option>
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16 <option value="no">No</option>
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17 </param>
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18 <param name="out_format2" type="select">
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19 <label>Output Sequence File Format</label>
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20 <option value="fasta">FASTA (m)</option>
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21 <option value="acedb">ACeDB (m)</option>
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22 <option value="asn1">ASN.1 (m)</option>
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23 <option value="clustal">Clustal (m)</option>
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24 <option value="codata">CODATA (m)</option>
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25 <option value="embl">EMBL (m)</option>
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26 <option value="fitch">Fitch (m)</option>
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27 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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28 <option value="genbank">GENBANK (m)</option>
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29 <option value="gff">GFF (m)</option>
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30 <option value="hennig86">Hennig86 (m)</option>
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31 <option value="ig">Intelligenetics (m)</option>
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32 <option value="jackknifer">Jackknifer (m)</option>
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33 <option value="jackknifernon">Jackknifernon (m)</option>
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34 <option value="mega">Mega (m)</option>
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35 <option value="meganon">Meganon (m)</option>
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36 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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37 <option value="pir">NBRF (PIR) (m)</option>
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38 <option value="ncbi">NCBI style FASTA (m)</option>
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39 <option value="nexus">Nexus/PAUP (m)</option>
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40 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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41 <option value="phylip">PHYLIP interleaved (m)</option>
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42 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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43 <option value="selex">SELEX (m)</option>
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44 <option value="staden">Staden (s)</option>
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45 <option value="strider">DNA strider (m)</option>
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46 <option value="swiss">SwisProt entry (m)</option>
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47 <option value="text">Plain sequence (s)</option>
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48 <option value="treecon">Treecon (m)</option>
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49 </param>
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50 <param name="out_format3" type="select">
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51 <label>Output Feature File Format</label>
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52 <option value="gff">GFF</option>
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53 <option value="embl">EMBL</option>
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54 <option value="swiss">SwissProt</option>
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55 </param>
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56 </inputs>
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57 <outputs>
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58 <data format="checktrans" name="out_file1" />
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59 <data format="fasta" name="out_file2" />
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60 <data format="gff" name="out_file3" />
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61 </outputs>
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62 <!-- <tests>
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63 <test>
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64 <param name="input1" value="2.fasta"/>
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65 <param name="orfml" value="100"/>
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66 <param name="addlast" value="yes"/>
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67 <param name="out_format2" value="fasta"/>
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68 <param name="out_format3" value="gff"/>
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69 <output name="out_file1" file="emboss_checktrans_out1.txt"/>
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70 <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
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71 <output name="out_file3" file="emboss_checktrans_out3.gff"/>
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72 </test>
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73 </tests> -->
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74 <code file="emboss_format_corrector.py" />
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75 <help>
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76
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77 .. class:: warningmark
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78
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79 The input dataset needs to be sequences.
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80
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81 -----
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82
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83 You can view the original documentation here_.
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84
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85 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/checktrans.html
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86
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87 ------
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88
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89 **Citation**
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90
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91 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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92
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93 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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94 </help>
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95 </tool>