Mercurial > repos > iuc > last
comparison macros_last.xml @ 0:9a7e91fc6562 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
| author | iuc |
|---|---|
| date | Wed, 17 Jun 2020 14:50:21 -0400 |
| parents | |
| children | 8705e0d74a0f |
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| -1:000000000000 | 0:9a7e91fc6562 |
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| 1 <macros> | |
| 2 <token name="@LAST_CONDA_VERSION@">1021</token> | |
| 3 <token name="@LAST_HELP@"><![CDATA[ | |
| 4 Documentation : http://last.cbrc.jp/ | |
| 5 | |
| 6 LAST finds similar regions between sequences. | |
| 7 | |
| 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). | |
| 9 | |
| 10 LAST can: | |
| 11 - Handle big sequence data, e.g: | |
| 12 - Compare two vertebrate genomes. | |
| 13 - Align billions of DNA reads to a genome. | |
| 14 - Indicate the reliability of each aligned column. | |
| 15 - Use sequence quality data properly. | |
| 16 - Compare DNA to proteins, with frameshifts. | |
| 17 - Compare PSSMs to sequences. | |
| 18 - Calculate the likelihood of chance similarities between random sequences. | |
| 19 - Do split and spliced alignment. | |
| 20 - Train alignment parameters for unusual kinds of sequence (e.g. nanopore). | |
| 21 | |
| 22 ]]></token> | |
| 23 <xml name="citations"> | |
| 24 <citation type="doi">10.1101/gr.113985.110</citation> | |
| 25 </xml> | |
| 26 | |
| 27 <xml name="input_db"> | |
| 28 <conditional name="db_opts"> | |
| 29 <param name="db_opts_input" type="select" label="Reference database"> | |
| 30 <option value="db">Locally installed LAST database</option> | |
| 31 <option value="lastdb" selected="true">LAST database from history</option> | |
| 32 </param> | |
| 33 <when value="db"> | |
| 34 <param name="database" type="select" multiple="true" label="LAST database"> | |
| 35 <options from_data_table="lastdb" /> | |
| 36 </param> | |
| 37 </when> | |
| 38 <when value="lastdb"> | |
| 39 <param name="lastdatabase" type="data" label="LAST database" /> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 </xml> | |
| 43 | |
| 44 <xml name="step_macro" token_step="1"> | |
| 45 <param argument="-w" type="integer" value="@STEP@" label="Use initial matches starting at every w-th position in each sequence"/> | |
| 46 <param argument="-W" type="integer" value="1" label="Use minimum positions in sliding windows of W consecutive positions"/> | |
| 47 <!-- -m ignored if -u is defined scheme --> | |
| 48 <param argument="-m" type="integer" value="1" label="Seed pattern"/> | |
| 49 </xml> | |
| 50 | |
| 51 <xml name="score_macro"> | |
| 52 <section name="score_opt" title="Score options" expanded="false"> | |
| 53 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous"> | |
| 54 <option value="0" selected="true">Neither sequence</option> | |
| 55 <option value="1">Reference</option> | |
| 56 <option value="2">Query</option> | |
| 57 <option value="3">Both</option> | |
| 58 </param> | |
| 59 <!-- | |
| 60 <param name="residue_pair_cost" argument="-c" type="integer" value="0" label="Unaligned residue pair cost"/> | |
| 61 <param name="frameshift_cost" argument="-F" type="integer" value="0" label="Frameshift cost"/> | |
| 62 --> | |
| 63 <param argument="-x" type="integer" value="21" label="Maximum score drop for preliminary gapped alignments"/> | |
| 64 <param argument="-y" type="integer" value="9" label="Maximum score drop for gapless alignments"/> | |
| 65 <param argument="-z" type="integer" value="21" label="Maximum score drop for final gapped alignments"/> | |
| 66 <param argument="-d" type="integer" value="13" label="Minimum score for gapless alignments"/> | |
| 67 <param argument="-e" type="integer" value="22" label="Minimum score for gapped alignments"/> | |
| 68 </section> | |
| 69 </xml> | |
| 70 | |
| 71 <xml name="cost_macro" token_a="7" token_b="1"> | |
| 72 <section name="cost_opt" title="Cost options" expanded="false"> | |
| 73 <param argument="-a" type="integer" value="@A@" label="Gap existence cost"/> | |
| 74 <param argument="-b" type="integer" value="@B@" label="Gap extension cost"/> | |
| 75 <param argument="-A" type="integer" value="@A@" label="Insertion existence cost"/> | |
| 76 <param argument="-B" type="integer" value="@B@" label="Insertion extension cost"/> | |
| 77 </section> | |
| 78 </xml> | |
| 79 | |
| 80 </macros> |