changeset 12:68129ce1c59b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit 034af1aa838fb62aa93c10332b6143ab1a1f3cef

--- a/dada2_learnErrors.xml	Sat Dec 20 14:15:06 2025 +0000
+++ b/dada2_learnErrors.xml	Wed Mar 18 13:09:40 2026 +0000
@@ -23,8 +23,15 @@
 files <- c(files, '$read')
 #end for
 
+#if $advanced.errfoo != "BinnedQualErrfun"
+    errfoo<-$advanced.errfoo
+#else:
+    binnedQs <- c($advanced.quality_bins)
+    errfoo <- makeBinnedQualErrfun(binnedQs)
+#end if
+
 err <- learnErrors(files, nbases = 10**$nbases,
-           errorEstimationFunction = $advanced.errfoo, multithread = nthreads,
+           errorEstimationFunction = errfoo, multithread = nthreads,
            randomize = $advanced.randomize, MAX_CONSIST = $advanced.maxconsist, OMEGA_C = $advanced.omegac)
 
 saveRDS(err, file='$errors')
@@ -87,6 +94,25 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test binned error foo -->
+        <test>
+            <param name="fls" value="filterAndTrim_F3D0_R1.fq.gz,filterAndTrim_F3D141_R1.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="nbases" value="6" />
+            <param name="advanced|errfoo" value="BinnedQualErrfun" />
+            <param name="advanced|quality_bins" value="1,11,21,31,41" />
+            <output name="errors" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" compare="sim_size" delta="13000">
+                <assert_contents>
+                    <has_size min="1k"/>
+                </assert_contents>
+            </output>
+            <output name="plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="%PDF"/>
+                    <has_text text="%%EOF"/>
+                </assert_contents>
+            </output>
+        </test>
+
     </tests>
     <help><![CDATA[
 Description

--- a/macros.xml	Sat Dec 20 14:15:06 2025 +0000
+++ b/macros.xml	Wed Mar 18 13:09:40 2026 +0000
@@ -13,8 +13,8 @@
         </xrefs>
     </xml>
     <token name="@PROFILE@">24.2</token>
-    <token name="@TOOL_VERSION@">1.34.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.38.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[
@@ -116,6 +116,10 @@
             <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
             <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
             <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option>
+            <option value="BinnedQualErrfun">BinnedQualErrfun: Use piecewise linear fit to estimate error rates from transition counts derived from binned quality score data. </option>
+        </param>
+        <param name="quality_bins" type="text" value="" label="Quality bins" help="Quality bins to be used for BinnedQualErrfun">
+            <validator type="regex" message="Must be a comma separate list of numbers">|([0-9]+(,[0-9]+)+)</validator>
         </param>
     </xml>
     <token name="@HELP_OVERVIEW@"><![CDATA[