--- a/kobas_identify.xml	Thu Nov 10 16:21:41 2016 -0500
+++ b/kobas_identify.xml	Thu Nov 28 15:50:07 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="kobas_identify" name="KOBAS Identify" version="@WRAPPER_VERSION@">
+<tool id="kobas_identify" name="KOBAS Identify" version="@TOOL_VERSION@">
     <description>KEGG Orthology Based Annotation System</description>
     <macros>
         <import>kobas_macros.xml</import>
@@ -6,44 +6,41 @@
 
     <expand macro="requirements"/>
 
-    <command>
-        <![CDATA[
-
-        mkdir sqlite &&
-        mkdir seq_pep &&
+    <command><![CDATA[
+mkdir sqlite &&
+mkdir seq_pep &&
 
-        #if not isinstance( $db.value, list ):
-            #set $db_args = [ $db.value ]
-        #else:
-            #set $db_args = $db.value
-        #end if
-        #set $db_args = "/".join($db.value)
+#if not isinstance( $db.value, list ):
+    #set $db_args = [ $db.value ]
+#else:
+    #set $db_args = $db.value
+#end if
+#set $db_args = "/".join($db.value)
 
-        ln -s '$kobasdb' 'sqlite/${species}.db' &&
+ln -s '$kobasdb' 'sqlite/${species}.db' &&
 
-        kobas-identify
-            -f '$fgfile'
-            #if $bg.bgtype == 'file':
-                -b '$bg.bgfile'
-            #elif $bg.bgtype == 'species':
-                -b '$bg.bgspecies'
-            #end if
-            -d '$db_args'
-            -m '$method'
-            -n '$fdr'
-            -c $cutoff
-            -q sqlite
-            -p blastp
-            -x blastx
-            -o '$output'
-        ]]>
-    </command>
+kobas-identify
+-f '$fgfile'
+#if $bg.bgtype == 'file':
+    -b '$bg.bgfile'
+#elif $bg.bgtype == 'species':
+    -b '$bg.bgspecies'
+#end if
+-d '$db_args'
+-m '$method'
+-n '$fdr'
+-c $cutoff
+-q sqlite
+-p blastp
+-x blastx
+-o '$output'
+    ]]></command>
     <inputs>
-        <param format="tabular" type="data" label="Foreground" argument="--fgfile" help="Foreground file, the output of KOBAS Annotate"/>
+        <param argument="--fgfile" type="data" format="tabular" label="Foreground" help="Foreground file, the output of KOBAS Annotate"/>
 
         <expand macro="input_kobasdb"/>
 
-        <param type="select" label="Database" argument="--db" multiple="True" display="checkboxes" help="Select your desired databases:
+        <param type="select" label="Database" argument="--db" multiple="True" optional="false" display="checkboxes" help="Select your desired databases:
 (Note: the Corrected P-Values will be affected by the number of selected databases)">
             <option value="K">KEGG Pathway</option>
             <option value="n">PID</option>
@@ -58,15 +55,10 @@
             <option value="N">NHGRI GWAS Catalog</option>
             <option value="G">Gene Ontology</option>
             <option value="S">Gene Ontology Slim (GOslim)</option>
-            <validator type="no_options" message="You must pick at least one database."/>
         </param>
 
         <conditional name="bg">
-            <param
-                name="bgtype"
-                type="select"
-                argument="--bgfile"
-                label="Background"
+            <param name="bgtype" argument="--bgfile" type="select" label="Background"
                 help="Optional background file, the output of annotate (3 or 4-letter
                         file name is not allowed), or species abbreviation
                         (for example: hsa for Homo sapiens, mmu for Mus
@@ -80,13 +72,10 @@
             </param>
             <when value="same"></when>
             <when value="file">
-                <param format="txt" name="bgfile" type="data" label="Background file"/>
+                <param name="bgfile" type="data" format="txt" label="Background file"/>
             </when>
             <when value="species">
-                <param
-                    name="bgspecies"
-                    type="text"
-                    label="Species abbreviation"
+                <param name="bgspecies" type="text" label="Species abbreviation"
                     help="For example: ko for KEGG
                         Orthology, hsa for Homo sapiens, mmu for Mus musculus,
                         dme for Drosophila melanogaster, ath for Arabidopsis
@@ -102,18 +91,17 @@
             <option value="x">Frequency list</option>
         </param>
 
-        <param type="select" argument="--fdr" label="FDR" help="False discovery rate (FDR) correction method">
+        <param argument="--fdr" type="select" label="FDR" help="False discovery rate (FDR) correction method">
             <option selected="True" value="BH">Benjamini and Hochberg</option>
             <option value="BY">Benjamini and Yekutieli</option>
             <option value="QVALUE">QVALUE</option>
             <option value="None">None</option>
         </param>
 
-        <param type="integer" min="0" argument="--cutoff" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/>
-
+        <param argument="--cutoff" type="integer" min="0" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output"/>
+        <data name="output" format="tabular"/>
     </outputs>
 
     <tests>
@@ -125,7 +113,7 @@
             <conditional name="bg">
                 <param name="bgtype" value="same"/>
             </conditional>
-            <output name="out_file1" file="kobas_identify_output.txt"/>
+            <output name="output" file="kobas_identify_output.txt"/>
         </test>
     </tests>