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annotate macros_last.xml @ 3:3de2195f32c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
author iuc
date Fri, 13 Nov 2020 09:05:49 +0000
parents 9a7e91fc6562
children 8705e0d74a0f
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9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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1 <macros>
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2 <token name="@LAST_CONDA_VERSION@">1021</token>
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3 <token name="@LAST_HELP@"><![CDATA[
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4 Documentation : http://last.cbrc.jp/
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6 LAST finds similar regions between sequences.
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9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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8 The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds).
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9
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10 LAST can:
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11 - Handle big sequence data, e.g:
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12 - Compare two vertebrate genomes.
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13 - Align billions of DNA reads to a genome.
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14 - Indicate the reliability of each aligned column.
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15 - Use sequence quality data properly.
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16 - Compare DNA to proteins, with frameshifts.
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17 - Compare PSSMs to sequences.
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18 - Calculate the likelihood of chance similarities between random sequences.
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19 - Do split and spliced alignment.
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20 - Train alignment parameters for unusual kinds of sequence (e.g. nanopore).
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21
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22 ]]></token>
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23 <xml name="citations">
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24 <citation type="doi">10.1101/gr.113985.110</citation>
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25 </xml>
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26
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27 <xml name="input_db">
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28 <conditional name="db_opts">
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29 <param name="db_opts_input" type="select" label="Reference database">
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30 <option value="db">Locally installed LAST database</option>
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31 <option value="lastdb" selected="true">LAST database from history</option>
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32 </param>
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33 <when value="db">
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34 <param name="database" type="select" multiple="true" label="LAST database">
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35 <options from_data_table="lastdb" />
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36 </param>
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37 </when>
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38 <when value="lastdb">
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39 <param name="lastdatabase" type="data" label="LAST database" />
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40 </when>
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41 </conditional>
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42 </xml>
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43
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44 <xml name="step_macro" token_step="1">
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45 <param argument="-w" type="integer" value="@STEP@" label="Use initial matches starting at every w-th position in each sequence"/>
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46 <param argument="-W" type="integer" value="1" label="Use minimum positions in sliding windows of W consecutive positions"/>
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47 <!-- -m ignored if -u is defined scheme -->
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48 <param argument="-m" type="integer" value="1" label="Seed pattern"/>
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49 </xml>
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50
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51 <xml name="score_macro">
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52 <section name="score_opt" title="Score options" expanded="false">
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53 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous">
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54 <option value="0" selected="true">Neither sequence</option>
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55 <option value="1">Reference</option>
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56 <option value="2">Query</option>
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57 <option value="3">Both</option>
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58 </param>
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59 <!--
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60 <param name="residue_pair_cost" argument="-c" type="integer" value="0" label="Unaligned residue pair cost"/>
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61 <param name="frameshift_cost" argument="-F" type="integer" value="0" label="Frameshift cost"/>
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62 -->
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63 <param argument="-x" type="integer" value="21" label="Maximum score drop for preliminary gapped alignments"/>
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64 <param argument="-y" type="integer" value="9" label="Maximum score drop for gapless alignments"/>
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65 <param argument="-z" type="integer" value="21" label="Maximum score drop for final gapped alignments"/>
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66 <param argument="-d" type="integer" value="13" label="Minimum score for gapless alignments"/>
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67 <param argument="-e" type="integer" value="22" label="Minimum score for gapped alignments"/>
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68 </section>
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69 </xml>
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70
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71 <xml name="cost_macro" token_a="7" token_b="1">
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72 <section name="cost_opt" title="Cost options" expanded="false">
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73 <param argument="-a" type="integer" value="@A@" label="Gap existence cost"/>
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74 <param argument="-b" type="integer" value="@B@" label="Gap extension cost"/>
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75 <param argument="-A" type="integer" value="@A@" label="Insertion existence cost"/>
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76 <param argument="-B" type="integer" value="@B@" label="Insertion extension cost"/>
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77 </section>
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78 </xml>
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79
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80 </macros>