diff dada2_seqCounts.xml @ 2:f74c56549143 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"

--- a/dada2_seqCounts.xml	Thu Dec 05 18:01:18 2019 -0500
+++ b/dada2_seqCounts.xml	Mon Mar 16 08:13:07 2020 -0400
@@ -89,38 +89,38 @@
              names of the elements of the input collection for <param ... multiple="true">]) -->
         <test>
             <repeat name="inrep">
-                <param name="input" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
+                <param name="input" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
                 <param name="name" value="filter"/>
             </repeat>
-            <output name="counts" value="seqCounts_F3D0_filter.tab" ftype="tabular" />
+            <output name="counts" value="seqCounts_filter.tab" ftype="tabular" />
         </test>
         <test>
             <repeat name="inrep">
-                <param name="input" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
+                <param name="input" value="dada_F3D0_S188_L001_R1.Rdata,dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada"/>
                 <param name="name" value="dadaF"/>
             </repeat>
-            <output name="counts" value="seqCounts_F3D0_dadaF.tab" ftype="tabular" />
+            <output name="counts" value="seqCounts_dadaF.tab" ftype="tabular" />
         </test>
         <test>
             <repeat name="inrep">
-                <param name="input" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs"/>
+                <param name="input" value="mergePairs_F3D0_S188_L001.Rdata,mergePairs_F3D141_S207_L001.Rdata" ftype="dada2_mergepairs"/>
                 <param name="name" value="merge"/>
             </repeat>
-            <output name="counts" value="seqCounts_F3D0_merge.tab" ftype="tabular" />
+            <output name="counts" value="seqCounts_merge.tab" ftype="tabular" />
         </test>
         <test>
             <repeat name="inrep">
-                <param name="input" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="input" value="makeSequenceTable.tab" ftype="dada2_sequencetable"/>
                 <param name="name" value="seqtab"/>
             </repeat>
-            <output name="counts" value="seqCounts_F3D0_seqtab.tab" ftype="tabular" />
+            <output name="counts" value="seqCounts_seqtab.tab" ftype="tabular" />
         </test>
         <test>
             <repeat name="inrep">
-                <param name="input" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="input" value="removeBimeraDenovo.tab" ftype="dada2_sequencetable"/>
                 <param name="name" value="nochim"/>
             </repeat>
-            <output name="counts" value="seqCounts_F3D0_nochim.tab" ftype="tabular" />
+            <output name="counts" value="seqCounts_nochim.tab" ftype="tabular" />
         </test>
     </tests>
     <help><![CDATA[
@@ -135,7 +135,10 @@
 **Inputs:**
 
 Any number of results of dada2 steps in the following form:
-- a collection of results from dada, or mergePairs; or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
+
+
+- a collection of results from dada, mergePairs, or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
+- the results of dada in non-batch mode
 - the result of makeSequenceTable or removeBimeraDenovo
 
 **Output:**