diff dada2_seqCounts.xml @ 3:0c2c91057b4b draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty

--- a/dada2_seqCounts.xml	Tue Apr 09 07:09:26 2019 -0400
+++ b/dada2_seqCounts.xml	Mon Apr 29 09:00:08 2019 -0400
@@ -57,7 +57,7 @@
         }
         t <- tryCatch({
             sapply(samples, getN)
-        }, 
+        },
         error=function(cond) {
             rowSums(samples)
         })
@@ -73,7 +73,7 @@
     ]]></configfile>
     </configfiles>
     <inputs>
-		<repeat name="inrep" title="data sets" min="1">
+        <repeat name="inrep" title="data sets" min="1">
             <param name="input" type="data" multiple="true" format="tabular,@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="Dataset(s)"/>
             <param name="name" type="text" value="" optional="true" label="name"/>
         </repeat>
@@ -84,8 +84,14 @@
     <tests>
     </tests>
     <help><![CDATA[
+Description
+...........
+
 Get the counts of sequences per sample for the different stages of the dada pipeline.
 
+Usage
+.....
+
 **Inputs:**
 
 Any number of results from derepFastq, dada, mergePairs, makeSequenceTable, and removeBimeraDenovo. Additionally the statistics of filterAndTrim can be used.
@@ -94,12 +100,15 @@
 
 A table containing the number of sequences per sample (rows) for each input (columns)
 
-**Details**
+Details
+.......
 
-For results from 
+For results from
 
 - derepFastq, dada, and mergePairs the sum of the result of dada2's getUniques function is used
 - makeSequenceTable, and removeBimeraDenovo R's rowSums function is used
+
+@HELP_OVERVIEW@
     ]]></help>
     <expand macro="citations"/>
 </tool>