diff --git a/tools/spades/biosyntheticspades.xml b/tools/spades/biosyntheticspades.xml
index afaab415c1e..98789eac11a 100644
--- a/tools/spades/biosyntheticspades.xml
+++ b/tools/spades/biosyntheticspades.xml
@@ -67,7 +67,7 @@ spades.py --bio
         <!-- #1 single, interlaced, fastq.gz, default parameters -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <output name="out_b">
diff --git a/tools/spades/macros.xml b/tools/spades/macros.xml
index 6cb3d366596..13af7ec1f81 100644
--- a/tools/spades/macros.xml
+++ b/tools/spades/macros.xml
@@ -57,7 +57,18 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
     #return $ext
 #end def
 
-#if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
+#if $singlePaired.sPaired == "single"
+    mkdir -p reads1 &&
+    #set file_paths1 = []
+    #for $input_file in $singlePaired.input1
+        #set ext = $fix_ext($input_file.ext)
+        #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
+        #set file_path = 'reads1/' + $fname
+        ln -s '$input_file' '$file_path' &&
+        $file_paths1.append($file_path)
+    #end for
+
+#else if $singlePaired.sPaired == "single_collection"
     mkdir -p reads1 &&
     #set file_paths1 = []
     #for $input_file in $singlePaired.input1
@@ -67,7 +78,40 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
         ln -s '$input_file' '$file_path' &&
         $file_paths1.append($file_path)
     #end for
+
+#else if $singlePaired.sPaired == "interlaced"
+    mkdir -p reads1 &&
+    #set file_paths1 = []
+    #set ext = $fix_ext($singlePaired.input_interlaced.ext)
+    #set file_path = 'reads1/interlaced.' + $ext
+    ln -s '$singlePaired.input_interlaced' '$file_path' &&
+    $file_paths1.append($file_path)
+
+#else if $singlePaired.sPaired == "interlaced_collection"
+    mkdir -p reads1 &&
+    #set file_paths1 = []
+    #for $input_file in $singlePaired.input1
+        #set ext = $fix_ext($input_file.ext)
+        #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
+        #set file_path = 'reads1/' + $fname
+        ln -s '$input_file' '$file_path' &&
+        $file_paths1.append($file_path)
+    #end for
+
+#else if $singlePaired.sPaired == "paired"
+    mkdir -p paired_reads1 &&
+    #set fw_reads1 = []
+    #set rv_reads1 = []
+    #set ext = $fix_ext($singlePaired.input.forward.ext)
+    #set file_path_fw = 'paired_reads1/forward.' + $ext
+    ln -s '$singlePaired.input.forward' '$file_path_fw' &&
+    $fw_reads1.append($file_path_fw)
+    #set file_path_rv = 'paired_reads1/reverse.' + $ext
+    ln -s '$singlePaired.input.reverse' '$file_path_rv' &&
+    $rv_reads1.append($file_path_rv)
+
 #else
+    ## paired_collection
     mkdir -p paired_reads1 &&
     #set fw_reads1 = []
     #set rv_reads1 = []
@@ -84,7 +128,26 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
 ]]></token>
 
 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
-#if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
+#if $additional_reads.singlePaired.sPaired == "single"
+    mkdir -p reads2 &&
+    #set file_paths2 = []
+    #for $input_file in $additional_reads.singlePaired.input1
+        #set ext = $fix_ext($input_file.ext)
+        #set fname = re.sub('[^\w\-_.]', '_', $input_file.element_identifier) + '.' + $ext
+        #set file_path = 'reads2/' + $fname
+        ln -s '$input_file' '$file_path' &&
+        $file_paths2.append($file_path)
+    #end for
+
+#else if $additional_reads.singlePaired.sPaired == "interlaced"
+    mkdir -p reads2 &&
+    #set file_paths2 = []
+    #set ext = $fix_ext($additional_reads.singlePaired.input_interlaced.ext)
+    #set file_path = 'reads2/interlaced.' + $ext
+    ln -s '$additional_reads.singlePaired.input_interlaced' '$file_path' &&
+    $file_paths2.append($file_path)
+
+#else if $additional_reads.singlePaired.sPaired == "interlaced_collection"
     mkdir -p reads2 &&
     #set file_paths2 = []
     #for $input_file in $additional_reads.singlePaired.input1
@@ -94,7 +157,21 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
         ln -s '$input_file' '$file_path' &&
         $file_paths2.append($file_path)
     #end for
+
+#else if $additional_reads.singlePaired.sPaired == "paired"
+    mkdir -p paired_reads2 &&
+    #set fw_reads2 = []
+    #set rv_reads2 = []
+    #set ext = $fix_ext($additional_reads.singlePaired.input.forward.ext)
+    #set file_path_fw = 'paired_reads2/forward.' + $ext
+    ln -s '$additional_reads.singlePaired.input.forward' '$file_path_fw' &&
+    $fw_reads2.append($file_path_fw)
+    #set file_path_rv = 'paired_reads2/reverse.' + $ext
+    ln -s '$additional_reads.singlePaired.input.reverse' '$file_path_rv' &&
+    $rv_reads2.append($file_path_rv)
+
 #else
+    ## paired_collection
     mkdir -p paired_reads2 &&
     #set fw_reads2 = []
     #set rv_reads2 = []
@@ -123,12 +200,30 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
     #for $read in $file_paths1
         --s $library '${read}'
     #end for
-#else if $singlePaired.sPaired == "paired_interlaced"
+
+#else if $singlePaired.sPaired == "interlaced"
+    #for $read in $file_paths1
+        --${singlePaired.type_paired}-12 $library '${read}'
+        --${singlePaired.type_paired}-or $library $singlePaired.orientation
+    #end for
+
+#else if $singlePaired.sPaired == "interlaced_collection"
     #for $read in $file_paths1
         --${singlePaired.type_paired}-12 $library '${read}'
         --${singlePaired.type_paired}-or $library $singlePaired.orientation
     #end for
+
+#else if $singlePaired.sPaired == "paired"
+    #for $read in $fw_reads1
+        --${singlePaired.type_paired}-1 $library '${read}'
+    #end for
+    #for $read in $rv_reads1
+        --${singlePaired.type_paired}-2 $library '${read}'
+        --${singlePaired.type_paired}-or $library $singlePaired.orientation
+    #end for
+
 #else
+    ## paired_collection
     #for $read in $fw_reads1
         --${singlePaired.type_paired}-1 $library '${read}'
     #end for
@@ -139,19 +234,21 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
 #end if
 ]]></token>
 
-
 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
 @LIBRARY_NUMBER@
 #if $additional_reads.singlePaired.sPaired == "single"
     #for $read in $file_paths2
         --s $library '${read}'
     #end for
-#else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
+
+#else if $additional_reads.singlePaired.sPaired == "interlaced" or $additional_reads.singlePaired.sPaired == "interlaced_collection"
     #for $read in $file_paths2
         --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
         --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
     #end for
+
 #else
+    ## paired + paired_collection
     #for $read in $fw_reads2
         --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
     #end for
@@ -349,19 +446,47 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
 
     <xml name="input_files_all" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
         <conditional name="singlePaired">
-            <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
-                <option value="single">Single-end</option>
-                <option value="paired_interlaced">Paired-end: interlaced reads</option>
-                <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
+            <param name="sPaired" type="select" label="Input format for reads" help="@HELP@">
+                <option value="single">Single-end (individual assembly)</option>
+                <option value="paired">Paired-end: forward + reverse (individual assembly)</option>
+                <option value="interlaced">Paired-end: interlaced reads (individual assembly)</option>
+                <option value="single_collection">Single-end (co-assembly)</option>
+                <option value="interlaced_collection">Paired-end: interlaced reads (co-assembly)</option>
+                <option value="paired_collection" selected="true">Paired-end: list of dataset pairs (co-assembly)</option>
             </param>
+
+            <!-- single-end individual -->
             <when value="single">
-                <param format="@FORMAT@" name="input1" type="data"  multiple="true" label="@LABEL@"/>
+                <param format="@FORMAT@" name="input_single" type="data" label="@LABEL@: single-end"/>
             </when>
-            <when value="paired_interlaced">
-                <param format="@FORMAT@" name="input1" type="data"  multiple="true" label="@LABEL@: interlaced"/>
+
+            <!-- paired individual -->
+            <when value="paired">
+                <param format="@FORMAT@" name="input" type="data_collection" collection_type="paired" label="@LABEL@: paired reads"/>
                 <expand macro="type_paired"/>
                 <expand macro="orientation"/>
             </when>
+
+            <!-- interlaced individual -->
+            <when value="interlaced">
+                <param format="@FORMAT@" name="input_interlaced" type="data" label="@LABEL@: interlaced reads"/>
+                <expand macro="type_paired"/>
+                <expand macro="orientation"/>
+            </when>
+
+            <!-- single-end collection -->
+            <when value="single_collection">
+                <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: single-end"/>
+            </when>
+
+            <!-- interlaced collection -->
+            <when value="interlaced_collection">
+                <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
+                <expand macro="type_paired"/>
+                <expand macro="orientation"/>
+            </when>
+
+            <!-- paired collection -->
             <when value="paired_collection">
                 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
                 <expand macro="type_paired"/>
@@ -373,20 +498,50 @@ export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
     <xml name="input_files_paired" tokens="format,label" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
         <conditional name="singlePaired">
             <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
-                <option value="paired_interlaced">Paired-end: interlaced reads</option>
-                <option value="paired_collection" selected="true">Paired-end: list of dataset pairs</option>
+                <option value="paired">Paired-end: forward + reverse (individual assembly)</option>
+                <option value="interlaced">Paired-end: interlaced reads (individual assembly)</option>
+                <option value="interlaced_collection">Paired-end: interlaced reads (co-assembly)</option>
+                <option value="paired_collection" selected="true">Paired-end: list of dataset pairs (co-assembly)</option>
             </param>
-            <when value="paired_interlaced">
-                <param format="@FORMAT@" name="input1" type="data"  multiple="true" label="@LABEL@: interlaced"/>
+
+            <!-- single paired -->
+            <when value="paired">
+                <param name="input"
+                    type="data_collection"
+                    collection_type="paired"
+                    format="@FORMAT@"
+                    label="@LABEL@: paired reads"
+                    help="Provide one paired dataset with forward (R1) and reverse (R2) reads."/>
+                <expand macro="type_paired"/>
+                <expand macro="orientation"/>
+            </when>
+
+            <!-- single interlaced -->
+            <when value="interlaced">
+                <param name="input_interlaced"
+                    type="data"
+                    format="@FORMAT@"
+                    label="@LABEL@: interlaced reads"
+                    help="Provide a single file with interleaved forward and reverse reads."/>
                 <expand macro="type_paired"/>
                 <expand macro="orientation"/>
             </when>
+
+            <!-- multiple interlaced -->
+            <when value="interlaced_collection">
+                <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
+                <expand macro="type_paired"/>
+                <expand macro="orientation"/>
+            </when>
+
+            <!-- collection -->
             <when value="paired_collection">
                 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
                 <expand macro="type_paired"/>
                 <expand macro="orientation"/>
             </when>
         </conditional>
+
         <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the same sample, it means that they belong to the same library.">
             <option value="true" selected="true">True</option>
             <option value="false">False</option>
diff --git a/tools/spades/metaspades.xml b/tools/spades/metaspades.xml
index a629ff4b63a..e207907dc65 100755
--- a/tools/spades/metaspades.xml
+++ b/tools/spades/metaspades.xml
@@ -66,7 +66,7 @@ metaspades.py
         <!-- #1 single, interlaced, fastq.gz, default parameters -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <output name="out_ag">
@@ -141,7 +141,7 @@ metaspades.py
         <!-- #3 only corrected reads are created as an output -->
         <test expect_num_outputs="2">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="optional_output" value="cr,l"/>
diff --git a/tools/spades/plasmidspades.xml b/tools/spades/plasmidspades.xml
index 2fdcaa8da85..77d27da7bab 100644
--- a/tools/spades/plasmidspades.xml
+++ b/tools/spades/plasmidspades.xml
@@ -229,7 +229,7 @@ plasmidspades.py
         <test expect_num_outputs="1">
             <param name="operation_mode" value="--only-assembler"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <conditional name="additional_reads">
diff --git a/tools/spades/rnaspades.xml b/tools/spades/rnaspades.xml
index e3079d39a91..1ad5d5062fb 100644
--- a/tools/spades/rnaspades.xml
+++ b/tools/spades/rnaspades.xml
@@ -99,7 +99,7 @@ rnaspades.py
         <!-- #1 -->
         <test expect_num_outputs="1">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <output name="out_tr">
diff --git a/tools/spades/rnaviralspades.xml b/tools/spades/rnaviralspades.xml
index 1d678d9f04c..994ef1af25d 100644
--- a/tools/spades/rnaviralspades.xml
+++ b/tools/spades/rnaviralspades.xml
@@ -87,7 +87,7 @@ spades.py --rnaviral
         <!-- #1 single, interlaced, fastq.gz, default parameters -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <output name="out_ag">
diff --git a/tools/spades/spades.xml b/tools/spades/spades.xml
index d9278d53763..a00f9d8b018 100644
--- a/tools/spades/spades.xml
+++ b/tools/spades/spades.xml
@@ -94,7 +94,7 @@ spades.py
         <!-- #1 single, interlaced, fastq.gz, default parameters -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <output name="out_ag">
@@ -349,7 +349,7 @@ spades.py
         <test expect_num_outputs="2">
             <param name="operation_mode" value="--only-error-correction"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="mode_sel" value="--careful"/>
@@ -381,7 +381,7 @@ spades.py
         <test expect_num_outputs="2">
             <param name="operation_mode" value="--only-error-correction"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="mode_sel" value="--careful,--sc"/>
@@ -413,7 +413,7 @@ spades.py
         <test expect_num_outputs="4">
             <param name="operation_mode" value="--only-assembler"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="mode_sel" value="--sc"/>
@@ -448,7 +448,7 @@ spades.py
         <test expect_num_outputs="2">
             <param name="operation_mode" value="--only-error-correction"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="optional_output" value="cr,l"/>
@@ -479,7 +479,7 @@ spades.py
         <test expect_num_outputs="2">
             <param name="operation_mode" value="--only-error-correction"/>
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="mode_sel" value="--sc"/>
@@ -510,7 +510,7 @@ spades.py
         <!-- #11 -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <param name="mode_sel" value="--sc"/>
@@ -631,7 +631,7 @@ spades.py
         <!-- #14 interlaced, fastq.gz, hybrid assembly: nanopore, pacbio sanger and trustedcontigs -->
         <test expect_num_outputs="4">
             <conditional name="singlePaired">
-                <param name="sPaired" value="paired_interlaced"/>
+                <param name="sPaired" value="interlaced_collection"/>
                 <param name="input1" value="ecoli_1K.fastq.gz"/>
             </conditional>
             <section name="arf">