--- a/macros.xml	Tue Oct 05 20:05:50 2021 +0000
+++ b/macros.xml	Thu Nov 11 16:37:48 2021 +0000
@@ -31,6 +31,25 @@
             </conditional>
         </actions>
     </macro>
+    <macro name="input_type_cond">
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
+                <option value="single" selected="true">Single dataset</option>
+                <option value="pair">Dataset pair</option>
+                <option value="paired">List of dataset pairs</option>
+            </param>
+            <when value="single">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
+            </when>
+            <when value="pair">
+                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/>
+                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/>
+            </when>
+            <when value="paired">
+                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
+            </when>
+        </conditional>
+    </macro>
     <macro name="reference_source_cond">
         <conditional name="ref_source_cond">
             <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
@@ -46,10 +65,24 @@
                 </param>
             </when>
             <when value="history">
-                <param name="reference" type="data" format="fasta" label="Using reference genome">
-                    <validator type="no_options" message="The current history does not include a fasta dataset"/>
+                <param name="reference" type="data" format="fasta" label="Using reference genome"/>
+            </when>
+        </conditional>
+    </macro>
+    <macro name="ktrim_cond">
+        <conditional name="ktrim_cond">
+            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param argument="ktrim"  type="select" label="Select trimming position">
+                    <option value="r">Trim to the right</option>
+                    <option value="l">Trim to the left</option>
                 </param>
-            </when>
+                <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
+             </when>
         </conditional>
     </macro>
     <xml name="citations">