Mercurial > repos > iuc > last
view macros_last.xml @ 6:19c265784f35 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
author | iuc |
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date | Sat, 27 Nov 2021 10:12:45 +0000 |
parents | f5a5a2b39ff2 |
children | eca7ac1eb423 |
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<macros> <token name="@TOOL_VERSION@">1205</token> <token name="@LAST_HELP@"><![CDATA[ Documentation : http://last.cbrc.jp/ LAST finds similar regions between sequences. 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). LAST can: - Handle big sequence data, e.g: - Compare two vertebrate genomes. - Align billions of DNA reads to a genome. - Indicate the reliability of each aligned column. - Use sequence quality data properly. - Compare DNA to proteins, with frameshifts. - Compare PSSMs to sequences. - Calculate the likelihood of chance similarities between random sequences. - Do split and spliced alignment. - Train alignment parameters for unusual kinds of sequence (e.g. nanopore). ]]></token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">last</xref> </xrefs> </xml> <xml name="citations"> <citation type="doi">10.1101/gr.113985.110</citation> </xml> <xml name="input_db"> <conditional name="db_opts"> <param name="db_opts_input" type="select" label="Reference database"> <option value="db">Locally installed LAST database</option> <option value="lastdb" selected="true">LAST database from history</option> </param> <when value="db"> <param name="database" type="select" multiple="true" label="LAST database"> <options from_data_table="lastdb" /> </param> </when> <when value="lastdb"> <param name="lastdatabase" type="data" format="lastdb" label="LAST database" /> </when> </conditional> </xml> <xml name="step_macro" token_step="1"> <param argument="-w" type="integer" value="@STEP@" label="Use initial matches starting at every w-th position in each sequence"/> <param argument="-W" type="integer" value="1" label="Use minimum positions in sliding windows of W consecutive positions"/> <!-- -m ignored if -u is defined scheme --> <param argument="-m" type="integer" value="1" label="Seed pattern"/> </xml> <xml name="score_macro"> <section name="score_opt" title="Score options" expanded="false"> <param argument="-X" type="select" multiple="false" label="N/X is ambiguous"> <option value="0" selected="true">Neither sequence</option> <option value="1">Reference</option> <option value="2">Query</option> <option value="3">Both</option> </param> <!-- <param name="residue_pair_cost" argument="-c" type="integer" value="0" label="Unaligned residue pair cost"/> <param name="frameshift_cost" argument="-F" type="integer" value="0" label="Frameshift cost"/> --> <param argument="-x" type="integer" value="21" label="Maximum score drop for preliminary gapped alignments"/> <param argument="-y" type="integer" value="9" label="Maximum score drop for gapless alignments"/> <param argument="-z" type="integer" value="21" label="Maximum score drop for final gapped alignments"/> <param argument="-d" type="integer" value="13" label="Minimum score for gapless alignments"/> <param argument="-e" type="integer" value="22" label="Minimum score for gapped alignments"/> </section> </xml> <xml name="cost_macro" token_a="7" token_b="1"> <section name="cost_opt" title="Cost options" expanded="false"> <param argument="-a" type="integer" value="@A@" label="Gap existence cost"/> <param argument="-b" type="integer" value="@B@" label="Gap extension cost"/> <param argument="-A" type="integer" value="@A@" label="Insertion existence cost"/> <param argument="-B" type="integer" value="@B@" label="Insertion extension cost"/> </section> </xml> </macros>