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Bump dada2 #6731

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merged 4 commits into from
Feb 11, 2025
+19 −17
Merged

Bump dada2 #6731

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e32df53
add comment on pooled chimera removal
bernt-matthias Feb 10, 2025
76f4b4d
use standard macro token names and add profile token
bernt-matthias Feb 10, 2025
7fc6378
bump
bernt-matthias Feb 10, 2025
67c8528
workaround link
bernt-matthias Feb 11, 2025
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_assignTaxonomyAddspecies.xml
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<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Learn Error rates</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_dada.xml
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<tool id="dada2_dada" name="dada2: dada" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_dada" name="dada2: dada" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Remove sequencing errors</description>
<macros>
<import>macros.xml</import>
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7 changes: 3 additions & 4 deletions tools/dada2/dada2_filterAndTrim.xml
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<tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Filter and trim short read data</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -294,8 +294,7 @@ Details

- Truncation of the read length is enforced after trimming of the right end.
- The long read filter is applied before trimming and the short read filter after trimming.
- For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401

- For details on the calculation of the number of expected errors see also Calahan et al. 2016

*String present at the start of valid reads* (orient.fwd):

Expand All @@ -316,4 +315,4 @@ This step may be replaced by alternative tools to filter and trim short read dat
@HELP_OVERVIEW@
]]></help>
<expand macro="citations"/>
</tool>
</tool>
2 changes: 1 addition & 1 deletion tools/dada2/dada2_learnErrors.xml
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<tool id="dada2_learnErrors" name="dada2: learnErrors" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_learnErrors" name="dada2: learnErrors" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Learn Error rates</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_makeSequenceTable.xml
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<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>construct a sequence table (analogous to OTU table)</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_mergePairs.xml
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<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Merge denoised forward and reverse reads</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_plotComplexity.xml
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<tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Plot sequence complexity profile</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_plotQualityProfile.xml
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<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>plot a visual summary of the quality scores</description>
<macros>
<import>macros.xml</import>
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2 changes: 1 addition & 1 deletion tools/dada2/dada2_primercheck.xml
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<tool id="dada2_primerCheck" name="dada2: primer check" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_primerCheck" name="dada2: primer check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description></description>
<macros>
<import>macros.xml</import>
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4 changes: 3 additions & 1 deletion tools/dada2/dada2_removeBimeraDenovo.xml
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<tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Remove bimeras from collections of unique sequences</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -82,6 +82,8 @@ This tool can be used to remove chimeric sequences, i.e. sequences that can be c
- from **pooled** sequences: Each sequence is evaluated against a set of "parents" drawn from the sequence collection that are sufficiently more abundant than the sequence being evaluated. Sequences that are bimera are removed, i.e. a two-parent chimera, in which the left side is made up of one parent sequence, and the right-side made up of a second parent sequence.
- by **consensus**: In short, bimeric sequences are flagged on a sample-by-sample basis. Then, a vote is performed for each sequence across all samples in which it appeared. If the sequence is flagged in a sufficiently high fraction of samples, it is identified as a bimera. A logical vector is returned, with an entry for each sequence in the table indicating whether it was identified as bimeric by this consensus procedure.

**Note**: pooled should only be used in combination with pooled denoising.

Usage
.....

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2 changes: 1 addition & 1 deletion tools/dada2/dada2_seqCounts.xml
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<tool id="dada2_seqCounts" name="dada2: sequence counts" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
<tool id="dada2_seqCounts" name="dada2: sequence counts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description></description>
<macros>
<import>macros.xml</import>
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7 changes: 4 additions & 3 deletions tools/dada2/macros.xml
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Expand Up @@ -2,7 +2,7 @@
<macros>
<xml name="requirements">
<requirements>
<requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
<requirement type="package" version="@TOOL_VERSION@">bioconductor-dada2</requirement>
<yield/>
</requirements>
</xml>
Expand All @@ -12,8 +12,9 @@
<xref type="bioconductor">dada2</xref>
</xrefs>
</xml>
<token name="@DADA2_VERSION@">1.30.0</token>
<token name="@WRAPPER_VERSION@">0</token>
<token name="@PROFILE@">23.2</token>
<token name="@TOOL_VERSION@">1.34.0</token>
<token name="@VERSION_SUFFIX@">0</token>

<xml name="version_command">
<version_command><![CDATA[
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