--- a/kobas_annotate.xml	Thu Nov 10 16:21:41 2016 -0500
+++ b/kobas_annotate.xml	Thu Nov 28 15:50:07 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
+<tool id="kobas_annotate" name="KOBAS Annotate" version="@TOOL_VERSION@">
     <description>KEGG Orthology Based Annotation System</description>
     <macros>
         <import>kobas_macros.xml</import>
@@ -10,78 +10,74 @@
         <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
         <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
     </stdio>
-    <command>
-        <![CDATA[
-
-        ## create the KOBAS directories
-        mkdir sqlite &&
-        mkdir seq_pep &&
+    <command><![CDATA[
+## create the KOBAS directories
+mkdir sqlite &&
+mkdir seq_pep &&
 
-        #if $blast_opts.choice == 'local':
-            #set $blast_path = $blast_opts.localdb.fields.path
-        #else if $blast_opts.choice == 'fasta':
-            makeblastdb
-                -in '$blast_opts.fastadb'
-                -dbtype 'prot'
-                -out 'seq_pep/${species}.pep.fasta' &&
-        #else:
-            #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
-        #end if
+#if $blast_opts.choice == 'local':
+    #set $blast_path = $blast_opts.localdb.fields.path
+#elif $blast_opts.choice == 'fasta':
+    makeblastdb
+        -in '$blast_opts.fastadb'
+        -dbtype 'prot'
+        -out 'seq_pep/${species}.pep.fasta' &&
+#else:
+    #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
+#end if
 
-        ## create the database symlinks to comply with how KOBAS wants them
-        ln -s '$organismdb' sqlite/organism.db &&
-        ln -s '$kobasdb' 'sqlite/${species}.db' &&
+## create the database symlinks to comply with how KOBAS wants them
+ln -s '$organismdb' sqlite/organism.db &&
+ln -s '$kobasdb' 'sqlite/${species}.db' &&
 
-        #if $blast_opts.choice != 'fasta':
-            ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
-            ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
-            ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
-        #end if
+#if $blast_opts.choice != 'fasta':
+    ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
+    ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
+    ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
+#end if
 
-        ## create the orthologe database symlinks to comply with how KOBAS wants them
-        #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
+## create the orthologe database symlinks to comply with how KOBAS wants them
+#if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
 
-            #if $ortholog.blast_opts_ortholog.choice == 'local':
-                #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
-            #else if $ortholog.blast_opts_ortholog.choice == 'fasta':
-                makeblastdb
-                    -in '$ortholog.blast_opts_ortholog.fastadb'
-                    -dbtype 'prot'
-                    -out 'seq_pep/${ortholog.species}.pep.fasta' &&
-            #else:
-                #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
-            #end if
+    #if $ortholog.blast_opts_ortholog.choice == 'local':
+        #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
+    #elif $ortholog.blast_opts_ortholog.choice == 'fasta':
+        makeblastdb
+            -in '$ortholog.blast_opts_ortholog.fastadb'
+            -dbtype 'prot'
+            -out 'seq_pep/${ortholog.species}.pep.fasta' &&
+    #else:
+        #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
+    #end if
 
-            ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
+    ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
 
-            #if $blast_opts.choice != 'fasta':
-                ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
-                ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
-                ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
-            #end if
-        #end if
+    #if $blast_opts.choice != 'fasta':
+        ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
+        ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
+        ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
+    #end if
+#end if
 
-        kobas-annotate
-            -i '$infile'
-            -t '$intype'
-            -s '$species'
-            -e '$evalue'
-            -r $rank
-            -n "\${GALAXY_SLOTS:-4}"
-            -c $coverage
-            #if $ortholog.only == 'YES':
-                -z '$ortholog.species'
-            #end if
-            -y seq_pep
-            -q sqlite
-            -p blastp
-            -x blastx
-            -o '$output'
-
-        ]]>
-    </command>
+kobas-annotate
+-i '$infile'
+-t '$intype'
+-s '$species'
+-e '$evalue'
+-r $rank
+-n "\${GALAXY_SLOTS:-4}"
+-c $coverage
+#if $ortholog.only == 'YES':
+    -z '$ortholog.species'
+#end if
+-y seq_pep
+-q sqlite
+-p blastp
+-x blastx
+-o '$output'
+    ]]></command>
     <inputs>
-        <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
+        <param argument="--infile" type="data" format="fasta,tabular,txt" label="Input file" help="Input data file matching the input type."/>
         <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
             <option value="fasta:pro">FASTA protein sequence</option>
             <option value="fasta:nuc">FASTA nucleotide sequence</option>
@@ -99,12 +95,12 @@
 
         <expand macro="input_kobasdb"/>
 
-        <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
-        <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
-        <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
-        <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
+        <param name="organismdb" type="data" format="sqlite" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
+        <param argument="--evalue" type="text" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
+        <param argument="--rank" type="integer" min="0" value="5" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
+        <param argument="--coverage" type="integer" min="0" value="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
         <conditional name="ortholog">
-            <param name="only" type="select" argument="--ortholog" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">
+            <param name="only" argument="--ortholog" type="select" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">
                 <option value="NO">No</option>
                 <option value="YES">Yes</option>
             </param>
@@ -118,7 +114,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="output"/>
+        <data name="output" format="tabular"/>
     </outputs>
 
     <tests>
@@ -132,7 +128,7 @@
             <param name="species" value="aaa"/>
             <param name="kobasdb" value="aaa.db"/>
             <param name="organismdb" value="organism.db"/>
-            <output name="out_file1" file="kobas_annotate_output.txt"/>
+            <output name="output" file="kobas_annotate_output.txt"/>
         </test>
     </tests>