diff dada2_seqCounts.xml @ 5:39e27bd6d230 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

--- a/dada2_seqCounts.xml	Mon Apr 29 09:51:56 2019 -0400
+++ b/dada2_seqCounts.xml	Sun May 05 12:34:57 2019 -0400
@@ -19,11 +19,12 @@
 #for $i, $rep in enumerate($inrep)
     samples = list()
     #for $s in $rep.input:
-        #if len($rep.input) == 1
-            samples <- $read_data( $s )
-        #else
+        ## for collection input assume identifiers are sample names
+        #if $s.ext in ["tabular", "dada2_dada", "dada2_derep", "dada2_mergepairs"]
             sample_name <- '$s.element_identifier'
             samples[[sample_name]] <- $read_data( $s )
+        #else
+            samples <- $read_data( $s )
         #end if
         #if $s.ext == "tabular"
             tabular <- T
@@ -82,6 +83,51 @@
         <data name="counts" format="tabular" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
+        <!-- test for the separate inputs (didn't implement as single test using the repeat
+             since the sample name won't match anyway [galaxy does not allow to specify the 
+             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="name" value="filter"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_filter.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="derepFastq_F3D0_R1.Rdata" ftype="dada2_derep"/>
+                <param name="name" value="derepF"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_derepF.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
+                <param name="name" value="dadaF"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_dadaF.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs"/>
+                <param name="name" value="merge"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_merge.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="name" value="seqtab"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_seqtab.tab" ftype="tabular" />
+        </test>
+        <test>
+            <repeat name="inrep">
+                <param name="input" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable"/>
+                <param name="name" value="nochim"/>
+            </repeat>
+            <output name="counts" value="seqCounts_F3D0_nochim.tab" ftype="tabular" />
+        </test>
     </tests>
     <help><![CDATA[
 Description
@@ -94,7 +140,9 @@
 
 **Inputs:**
 
-Any number of results from derepFastq, dada, mergePairs, makeSequenceTable, and removeBimeraDenovo. Additionally the statistics of filterAndTrim can be used.
+Any number of results of dada2 steps in the following form: 
+- a collection of results from derep, dada, or mergePairs; or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
+- the result of makeSequenceTable or removeBimeraDenovo
 
 **Output:**