# HG changeset patch
# User nml
# Date 1575392894 18000
# Node ID 631e8eb3371e7f83c32dc8c50ea3e313cfa209df
# Parent  92e72350a3c59e9983e7864d380af715449d010a
"planemo upload for repository https://github.com/phac-nml/wade commit 3a5997b52566d197a5103e5a317ce2ed2837065e"

diff -r 92e72350a3c5 -r 631e8eb3371e wade.xml
--- a/wade.xml	Fri Nov 29 14:57:47 2019 -0500
+++ b/wade.xml	Tue Dec 03 12:08:14 2019 -0500
@@ -1,31 +1,44 @@
-<tool id="wade" name="Wade" version="0.2.4+galaxy0">
+<tool id="wade" name="Wade" version="0.2.4+galaxy1">
     <description>identify regions of interest</description>
     <requirements>
         <requirement type="package" version="0.2.4">wade</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 
-        #for $i in $input#
-          cp '$i' '$i.element_identifier' &&
-        #end for
+
+
+        #if $mode.type == 'GAS':
+
+          #for $i in $mode.input#
+            cp '$i' '$i.element_identifier' &&
+          #end for
+
+          #set $samples = ','.join([$i.element_identifier for $i in ( $mode.input )])
+          #set $subtype = $mode.subtype
 
-        #set $samples = ','.join([$i.element_identifier for $i in ( $input )])
+        #else:
+
+          #for $i in $mode.subtype_input.input#
+            cp '$i' '$i.element_identifier' &&
+          #end for
+
+          #set $samples = ','.join([$i.element_identifier for $i in ( $mode.subtype_input.input )])
+          #set $subtype = $mode.subtype_input.subtype
+
+        #end if
 
         Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'
 
         -d 'output'
+
         -o '$mode.type'
-        -t '$mode.subtype'
+
+        -t '$subtype'
 
         -s '$samples'
 
     ]]></command>
     <inputs>
-    <param name="input"
-        type="data" format="fasta"
-        optional="false"
-        multiple="true"
-        label="Contig Fasta file(s)"/>
     <conditional name="mode">
       <param name="type" type="select" label="Analysis Group">
         <option value="GAS">GAS</option>
@@ -33,6 +46,9 @@
         <option value="PNEUMO">PNEUMO</option>
       </param>
       <when value="GAS">
+
+        <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+
         <param name="subtype" type="select" label="Select specific analysis">
           <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
           <option value="EMM">EMM Typing</option>
@@ -40,8 +56,11 @@
           <option value="VFDB">VFDB (Virulence Factor Database)</option>
           <option value="MASTER">Master blaster</option>
         </param>
+
       </when>
       <when value="GONO">
+
+        <conditional name="subtype_input">
         <param name="subtype" type="select" label="Select specific analysis">
           <option value="MLST">MLST Type</option>
           <option value="NGMAST">NG-MAST Type</option>
@@ -49,8 +68,27 @@
           <option value="rRNA23S">23S rRNA Alleles</option>
           <option value="MASTER">Master blaster</option>
         </param>
+        <when value="rRNA23S">
+          <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
+        </when>
+        <when value="MLST">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="NGMAST">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="NGSTAR">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="MASTER">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        </conditional>
+
       </when>
       <when value="PNEUMO">
+
+        <conditional name="subtype_input">
         <param name="subtype" type="select" label="Select specific analysis">
           <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
           <option value="MLST">MLST Type</option>
@@ -58,6 +96,23 @@
           <option value="rRNA23S">23S rRNA Alleles</option>
           <option value="MASTER">Master blaster</option>
         </param>
+        <when value="rRNA23S">
+          <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
+        </when>
+        <when value="AMR">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="MLST">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="VFDB">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        <when value="MASTER">
+          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
+        </when>
+        </conditional>
+
       </when>
     </conditional>
     </inputs>