--- a/macros.xml	Fri Dec 04 22:05:07 2020 +0000
+++ b/macros.xml	Fri Jan 15 17:38:35 2021 +0000
@@ -5,7 +5,7 @@
     the index versions in sync, but you should manually adjust the +galaxy
     version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.6a</token>
+    <token name="@VERSION@">2.7.7a</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -33,7 +33,7 @@
             <edam_operation>operation_0292</edam_operation>
         </edam_operations>
     </xml>
-    
+
     <xml name="index_selection" token_with_gene_model="0">
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
@@ -132,6 +132,35 @@
         #end if
         #end if
         ]]></token>
+    <token name="@READSHANDLING@" ><![CDATA[
+    ## Check that the input pairs are of the same type
+    ## otherwise STARsolo will run for a long time and then error out.
+    ## We consume either repeats of two inputs R1 + R2
+    ## or a collection of paired reads.
+    #if str($sc.input_types.use) == "repeat":
+        #set $reads1 = []
+        #set $reads2 = []
+        #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
+            #assert $r1.datatype == $r2.datatype
+            #silent $reads1.append(str($r1))
+            #silent $reads2.append(str($r2))
+        #end for
+        #set $reads1 = ','.join($reads1)
+        #set $reads2 = ','.join($reads2)
+    #elif str($sc.input_types.use) == "list_paired":
+        #set $r1 = $sc.input_types.input_collection.forward
+        #set $r2 = $sc.input_types.input_collection.reverse
+        #set $reads1 = $r1
+        #set $reads2 = $r2
+    #end if
+    ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
+    ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
+    --readFilesIn $reads2 $reads1
+    --soloCBmatchWLtype $sc.soloCBmatchWLtype
+    #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
+        @FASTQ_GZ_OPTION@
+    #end if
+    ]]></token>
     <xml name="ref_selection">
         <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
         <!-- Currently, this parameter is not exposed in the wrapper,
@@ -148,4 +177,53 @@
             <yield />
         </stdio>
     </xml>
+    <xml name="input_selection">
+        <conditional name="input_types" >
+            <param name="use" type="select" label="Input Type" >
+                <option value="repeat" >Separate barcode and cDNA reads</option>
+                <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
+            </param>
+            <when value="repeat">
+                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data"  multiple="true"
+                label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
+                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data"  multiple="true"
+                label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
+            </when>
+            <when value="list_paired">
+                <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="input_selection_smart_seq">
+        <conditional name="input_types_smart_seq" >
+            <param name="use" type="select" label="Input Type" >
+                <option value="list_single_end" >Single-end FASTQ collection</option>
+                <option value="list_paired_end" >Paired FASTQ collection</option>
+            </param>
+            <when value="list_single_end">
+                <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
+            </when>
+            <when value="list_paired_end">
+                <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="umidedup_options">
+        <option value="1MM_All" selected="true">All</option>
+        <option value="1MM_Directional" >Directional</option>
+    </xml>
+    <xml name="anchor_types">
+        <option value="0">Read start</option>
+        <option value="1">Read end</option>
+        <option value="2">Adapter start</option>
+        <option value="3">Adapter end</option>
+    </xml>
+    <xml name="cb_match_wl_common">
+        <option value="Exact" >Exact</option>
+        <option value="1MM" >Single match</option>
+    </xml>
+    <xml name="cb_match_wl_cellranger">
+        <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
+        <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
+    </xml>
 </macros>