--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kma_map.xml	Thu Oct 03 01:10:37 2019 -0400
@@ -0,0 +1,60 @@
+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">kma</requirement>
+    </requirements>
+    <version_command>kma -v</version_command>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        kma
+            -t \${GALAXY_SLOTS:-1}
+	    -t_db '${kma_index.fields.path}'
+            #if $single_paired.single_paired_selector == 'yes'
+                -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
+            #elif $single_paired.single_paired_selector == "collection":
+                -ipe '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
+            #else:
+                -i '${single_paired.input_sequences}'
+            #end if
+            -o output
+	]]>
+    </command>
+    <inputs>
+        <conditional name="single_paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+                <option value="collection">Collection</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
+            </param>
+            <when value="collection">
+                <param format="fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
+            </when>
+            <when value="yes">
+                <param format="fastq" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
+                <param format="fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
+            </when>
+            <when value="no">
+                <param format="fastq" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
+            </when>
+        </conditional>
+	<param name="kma_index" type="select">
+	    <options from_data_table="kma_index">
+	        <validator type="no_options" message="No KMA index available" />
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+      <data name="res" label="result overview" format="tabular" from_work_dir="output.res" />
+      <data name="aln" label="consensus alignment" format="aln" from_work_dir="output.aln" />
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+      <![CDATA[
+      ]]>
+    </help>
+    <expand macro="citations" />
+</tool>