use standard macro token names and add profile token

galaxyproject · Feb 10, 2025 · 5bbd52d · 5bbd52d
1 parent e32df53
commit 5bbd52d
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Showing 12 changed files with 14 additions and 14 deletions.
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>

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>

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 +12,8 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.30.0</token>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@TOOL_VERSION@">1.30.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[