Bump dada2 (galaxyproject#6731)

bernt-matthias · web-flow · commit bbbc0e71b1db · 2025-02-12T00:06:06.000+01:00
* add comment on pooled chimera removal

* use standard macro token names and add profile token

* bump

* workaround link
diff --git a/tools/dada2/dada2_assignTaxonomyAddspecies.xml b/tools/dada2/dada2_assignTaxonomyAddspecies.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_dada.xml b/tools/dada2/dada2_dada.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_filterAndTrim.xml b/tools/dada2/dada2_filterAndTrim.xml
@@ -1,4 +1,4 @@
-<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>
@@ -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):
 
@@ -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>
diff --git a/tools/dada2/dada2_learnErrors.xml b/tools/dada2/dada2_learnErrors.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_makeSequenceTable.xml b/tools/dada2/dada2_makeSequenceTable.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_mergePairs.xml b/tools/dada2/dada2_mergePairs.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_plotComplexity.xml b/tools/dada2/dada2_plotComplexity.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_plotQualityProfile.xml b/tools/dada2/dada2_plotQualityProfile.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_primercheck.xml b/tools/dada2/dada2_primercheck.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/dada2_removeBimeraDenovo.xml b/tools/dada2/dada2_removeBimeraDenovo.xml
@@ -1,4 +1,4 @@
-<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>
@@ -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
 .....
 
diff --git a/tools/dada2/dada2_seqCounts.xml b/tools/dada2/dada2_seqCounts.xml
@@ -1,4 +1,4 @@
-<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>
diff --git a/tools/dada2/macros.xml b/tools/dada2/macros.xml
@@ -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>
@@ -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[

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>Learn Error rates</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_dada" name="dada2: dada" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_dada" name="dada2: dada" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>Remove sequencing errors</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_learnErrors" name="dada2: learnErrors" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_learnErrors" name="dada2: learnErrors" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>Learn Error rates</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>construct a sequence table (analogous to OTU table)</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_mergePairs" name="dada2: mergePairs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>Merge denoised forward and reverse reads</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_plotComplexity" name="dada2: plotComplexity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>Plot sequence complexity profile</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description>plot a visual summary of the quality scores</description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<tool id="dada2_primerCheck" name="dada2: primer check" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">`
	`1`	`+<tool id="dada2_primerCheck" name="dada2: primer check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">`
`2`	`2`	`<description></description>`
`3`	`3`	`<macros>`
`4`	`4`	`<import>macros.xml</import>`