Mercurial > repos > iuc > dada2_filterandtrim

comparison dada2_filterAndTrim.xml @ 9:46ca7fe29b3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
author iuc
date Tue, 11 Feb 2025 23:22:21 +0000
parents 5b1707c8da92
children 3efaa80a3e20
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8:5b1707c8da92 9:46ca7fe29b3e
1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09"> 1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Filter and trim short read data</description> 2 <description>Filter and trim short read data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
292 292
293 *Trimming and filtering*: 293 *Trimming and filtering*:
294 294
295 - Truncation of the read length is enforced after trimming of the right end. 295 - Truncation of the read length is enforced after trimming of the right end.
296 - The long read filter is applied before trimming and the short read filter after trimming. 296 - The long read filter is applied before trimming and the short read filter after trimming.
297 - For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401 297 - For details on the calculation of the number of expected errors see also Calahan et al. 2016
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300 *String present at the start of valid reads* (orient.fwd): 299 *String present at the start of valid reads* (orient.fwd):
301 300
302 This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads. 301 This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads.
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