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comparison ngmlr.xml @ 1:bb51c75a0157 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr commit 4a774c70198144dda9f63d4c4de600aa5c866b4c
author iuc
date Wed, 27 Jul 2022 09:34:02 +0000
parents 95e4757d8da7
children
comparison
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0:95e4757d8da7 1:bb51c75a0157
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="ngmlr" name="CoNvex" version="@VERSION@"> 2 <tool id="ngmlr" name="CoNvex" version="@VERSION@">
3 <xrefs>
4 <xref type="bio.tools">ngmlr</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@VERSION@">0.2.7</token> 7 <token name="@VERSION@">0.2.7</token>
5 <xml name="rg_validator"> 8 <xml name="rg_validator">
6 <validator type="expression" message="This field can only accept printable characters, with the exception of single and double quotes">value.isprintable() and '"' not in value and "'" not in value</validator> 9 <validator type="expression" message="This field can only accept printable characters, with the exception of single and double quotes">value.isprintable() and '"' not in value and "'" not in value</validator>
7 </xml> 10 </xml>
146 </outputs> 149 </outputs>
147 <tests> 150 <tests>
148 <test> 151 <test>
149 <param name="reference" value="ngmlr-ref1.fa" /> 152 <param name="reference" value="ngmlr-ref1.fa" />
150 <param name="query" value="ngmlr-in1.fa" /> 153 <param name="query" value="ngmlr-in1.fa" />
151 <output name="alignments" file="ngmlr-out1.sam" lines_diff="2" /> 154 <output name="alignments" file="ngmlr-out1.sam" lines_diff="2" sort="true" />
152 </test> 155 </test>
153 <test> 156 <test>
154 <param name="reference" value="ngmlr-ref2.fa" /> 157 <param name="reference" value="ngmlr-ref2.fa" />
155 <param name="query" value="ngmlr-in2.fa" /> 158 <param name="query" value="ngmlr-in2.fa" />
156 <output name="alignments" file="ngmlr-out2.sam" lines_diff="2" /> 159 <output name="alignments" file="ngmlr-out2.sam" lines_diff="2" sort="true" />
157 </test> 160 </test>
158 <test> 161 <test>
159 <param name="reference" value="ngmlr-ref3.fa.gz" /> 162 <param name="reference" value="ngmlr-ref3.fa.gz" />
160 <param name="query" value="ngmlr-in3.fa.gz" /> 163 <param name="query" value="ngmlr-in3.fa.gz" />
161 <param name="min_residues" value="0.01" /> 164 <param name="min_residues" value="0.01" />
162 <output name="alignments" file="ngmlr-out3.sam" lines_diff="2" /> 165 <output name="alignments" file="ngmlr-out3.sam" lines_diff="2" sort="true" />
163 </test> 166 </test>
164 <test> 167 <test>
165 <param name="reference" value="ngmlr-ref3.fa.gz" /> 168 <param name="reference" value="ngmlr-ref3.fa.gz" />
166 <param name="query" value="ngmlr-in3.fa.gz" /> 169 <param name="query" value="ngmlr-in3.fa.gz" />
167 <output name="alignments" file="ngmlr-out4.sam" lines_diff="2" /> 170 <output name="alignments" file="ngmlr-out4.sam" lines_diff="2" sort="true" />
168 </test> 171 </test>
169 </tests> 172 </tests>
170 <help> 173 <help>
171 <![CDATA[ 174 <![CDATA[
172 CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions). 175 CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).