Dada2 add output (galaxyproject#6024)

* add some outputs for dada and merge * bump * fix bump seems that tag 1.30 does not exist at biocontainers
nilchia · May 24, 2024 · 9bbc089 · 9bbc089
1 parent 30f1030
commit 9bbc089
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Showing 3 changed files with 33 additions and 7 deletions.
diff --git a/tools/dada2/dada2_dada.xml b/tools/dada2/dada2_dada.xml
@@ -62,14 +62,18 @@ dada_result <- dada(derep, err,
 #if $batch_cond.batch_select == "no":
     #if len($batch_cond.derep) > 1:
     for( id in names(dada_result) ){
+        print(id)
+        print(dada_result[[id]])
         saveRDS(dada_result[[id]], file=file.path("output" ,paste(id, "dada2_dada", sep=".")))
     }
     #else
     #for $d in $batch_cond.derep:
+        print(dada_result)
         saveRDS(dada_result, file=file.path("output" ,paste('$d.element_identifier', "dada2_dada", sep=".")))
     #end for
     #end if
 #else
+        print(dada_result)
     saveRDS(dada_result, file='$dada')
 #end if
     ]]></configfile>
@@ -116,13 +120,19 @@ dada_result <- dada(derep, err,
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
                 <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
         <!-- default, batch -->
         <test expect_num_outputs="1">
             <param name="batch_cond|batch_select" value="yes"/>
             <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
             <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" />
             <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
        </test>
         <!-- test non-default options -->
         <test expect_num_outputs="1">
@@ -133,6 +143,9 @@ dada_result <- dada(derep, err,
             <output_collection name="data_collection" type="list">
                 <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
+            <assert_stdout>
+                <has_line line="43 sequence variants were inferred from 379 input unique sequences."/>
+            </assert_stdout>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/dada2/dada2_mergePairs.xml b/tools/dada2/dada2_mergePairs.xml
@@ -20,10 +20,12 @@ dadaR <- readRDS('$dadaR')
 merged <- mergePairs(dadaF, '$derepF', dadaR, '$derepR', minOverlap = $minOverlap, maxMismatch = $maxMismatch,
 ## currently not accessible by the wrapper    returnRejects = FALSE, propagateCol = character(0),
     justConcatenate = $justConcatenate, trimOverhang = $trimOverhang)
-
 saveRDS(merged, file='$merged')
-##For display in Galaxy this could be transposed (..but the user could also do it herself)
-##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T)
+#if $output_details
+    ##For display in Galaxy this could be transposed (..but the user could also do it herself)
+    merged <- apply(merged, 2, as.character)
+    write.table(merged, "$merged_details", quote=F, sep="\t", row.names = F, col.names = T)
+#end if
     ]]></configfile>
     </configfiles>
     <inputs>
@@ -35,20 +37,24 @@ saveRDS(merged, file='$merged')
         <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/>
         <param argument="justConcatenate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/>
         <param argument="trimOverhang" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/>
+        <param name="output_details" type="boolean" label="Output detailed table" help="Contains detailed information on the merged sequences, e.g. number of matched/mismatches"/>
     </inputs>
     <outputs>
         <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/>
+        <data name="merged_details" format="tabular" label="${tool.name} on ${on_string}: details">
+            <filter>output_details</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
             <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
             <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/>
             <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/>
             <output name="merged" value="mergePairs_F3D0_S188_L001.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400" />
         </test>
         <!-- test non-default options -->
-        <test>
+        <test expect_num_outputs="2">
             <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
             <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
             <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/>
@@ -58,6 +64,13 @@ saveRDS(merged, file='$merged')
             <param name="maxMismatch" value="1"/>
             <param name="justConcatenate" value="TRUE" />
             <param name="trimOverhang" value="TRUE" />
+            <param name="output_details" value="true"/>
+            <output name="merged_details">
+                <assert_contents>
+                    <has_n_lines n="50"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/dada2/macros.xml b/tools/dada2/macros.xml
@@ -12,8 +12,8 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.28</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@DADA2_VERSION@">1.30.0</token>
+    <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[