# HG changeset patch
# User matthias
# Date 1543581313 18000
# Node ID 02905edf00e4cb6a857e40fabc8b2f0fcd1d4623
# Parent  061c9e133d1eadd814218e372c3c88b3e8321d2e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

diff -r 061c9e133d1e -r 02905edf00e4 macros.xml
--- a/macros.xml	Thu Nov 29 11:43:50 2018 -0500
+++ b/macros.xml	Fri Nov 30 07:35:13 2018 -0500
@@ -2,12 +2,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">stacks</requirement>
+            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.2=he860b03_0</token>
+    <token name="@STACKS_VERSION@">2.2</token>
+    <token name="@WRAPPER_VERSION@">1</token>
 
     <xml name="stdio">
         <stdio>
@@ -174,22 +175,11 @@
 
     <!-- macro and token for BAM input-->
     <xml name="bam_input_macro">
-        <conditional name="input_type">
-            <param name="input_type_selector" type="select" label="BAM files">
-                <option value="list">data set list</option>
-                <option value="manual">data sets</option>
-            </param>
-            <when value="manual">
-                <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
-            </when>
-            <when value="list">
-                <param name="input_bam" format="bam" type="data_collection" collection_type="list" label="BAM files" />
-            </when>
-        </conditional>
+        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
     </xml>
     <token name="@BAM_INPUT@"><![CDATA[
     #set $bamlist = ""
-    #for $bam in $input_type.input_bam:
+    #for $bam in $input_bam:
         #set $filename = $clean_ext($bam.element_identifier)+".bam"
         #if re.search('.*\.bam$', $filename)
             ln -s '$bam' bam_inputs/$filename &&
diff -r 061c9e133d1e -r 02905edf00e4 stacks_shortreads.xml
--- a/stacks_shortreads.xml	Thu Nov 29 11:43:50 2018 -0500
+++ b/stacks_shortreads.xml	Fri Nov 30 07:35:13 2018 -0500
@@ -1,5 +1,5 @@
 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
-<tool id="stacks2_shortreads" name="Stacks2: process shortreads" version="@WRAPPER_VERSION@">
+<tool id="stacks2_shortreads" name="Stacks2: process shortreads" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
     <macros>
         <import>macros.xml</import>