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1 <tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
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2 <description>Trim ambiguous bits off the ends of sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -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>Sequences</label>
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8 </param>
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9 <param name="window" size="4" type="text" value="1">
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10 <label>Window size</label>
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11 </param>
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12 <param name="percent" size="5" type="text" value="100.0">
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13 <label>Threshold of the percentage ambiguity</label>
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14 </param>
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15 <param name="strict" type="select">
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16 <label>Trim all ambiguity codes</label>
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17 <option value="no">No</option>
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18 <option value="yes">Yes</option>
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19 </param>
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20 <param name="star" type="select">
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21 <label>In protein sequences, trim off not only X's, but also the *'s</label>
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22 <option value="no">No</option>
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23 <option value="yes">Yes</option>
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24 </param>
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25 <param name="left" type="select">
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26 <label>Trim at the start</label>
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27 <option value="yes">Yes</option>
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28 <option value="no">No</option>
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29 </param>
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30 <param name="right" type="select">
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31 <label>Trim at the end</label>
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32 <option value="yes">Yes</option>
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33 <option value="no">No</option>
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34 </param>
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35 <param name="out_format1" type="select">
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36 <label>Output Sequence File Format</label>
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37 <option value="fasta">FASTA (m)</option>
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38 <option value="acedb">ACeDB (m)</option>
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39 <option value="asn1">ASN.1 (m)</option>
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40 <option value="clustal">Clustal (m)</option>
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41 <option value="codata">CODATA (m)</option>
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42 <option value="embl">EMBL (m)</option>
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43 <option value="fitch">Fitch (m)</option>
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44 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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45 <option value="genbank">GENBANK (m)</option>
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46 <option value="gff">GFF (m)</option>
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47 <option value="hennig86">Hennig86 (m)</option>
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48 <option value="ig">Intelligenetics (m)</option>
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49 <option value="jackknifer">Jackknifer (m)</option>
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50 <option value="jackknifernon">Jackknifernon (m)</option>
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51 <option value="mega">Mega (m)</option>
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52 <option value="meganon">Meganon (m)</option>
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53 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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54 <option value="pir">NBRF (PIR) (m)</option>
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55 <option value="ncbi">NCBI style FASTA (m)</option>
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56 <option value="nexus">Nexus/PAUP (m)</option>
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57 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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58 <option value="phylip">PHYLIP interleaved (m)</option>
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59 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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60 <option value="selex">SELEX (m)</option>
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61 <option value="staden">Staden (s)</option>
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62 <option value="strider">DNA strider (m)</option>
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63 <option value="swiss">SwisProt entry (m)</option>
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64 <option value="text">Plain sequence (s)</option>
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65 <option value="treecon">Treecon (m)</option>
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66 </param>
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67 </inputs>
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68 <outputs>
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69 <data format="fasta" name="out_file1" />
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="input1" value="2.fasta"/>
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74 <param name="window" value="1"/>
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75 <param name="percent" value="100.0"/>
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76 <param name="strict" value="no"/>
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77 <param name="star" value="no"/>
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78 <param name="left" value="yes"/>
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79 <param name="right" value="yes"/>
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80 <param name="out_format1" value="fasta"/>
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81 <output name="out_file1" file="emboss_trimseq_out.fasta"/>
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82 </test>
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83 </tests>
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84 <code file="emboss_format_corrector.py" />
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85 <help>
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86
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87 .. class:: warningmark
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88
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89 The input dataset needs to be sequences.
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90
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91 -----
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92
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93 You can view the original documentation here_.
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94
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95 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html
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96 </help>
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97 </tool>
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