changeset 2:39ebc7633942 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty

--- a/macros.xml	Thu Nov 29 12:16:18 2018 -0500
+++ b/macros.xml	Fri Nov 30 07:30:43 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 &&

--- a/stacks_refmap.xml	Thu Nov 29 12:16:18 2018 -0500
+++ b/stacks_refmap.xml	Fri Nov 30 07:30:43 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="stacks2_refmap" name="Stacks2: reference map" version="@WRAPPER_VERSION@">
+<tool id="stacks2_refmap" name="Stacks2: reference map" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
     <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
     <macros>
         <import>macros.xml</import>
@@ -58,8 +58,7 @@
             <!-- TODO test for outputs -->
         </test>
         <test>
-            <param name="input_type|input_type_selector" value="manual"/>
-            <param name="input_type|input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
+            <param name="input_bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
             <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
             <param name="paired_select" value="--unpaired"/>
             <param name="model_options|var_alpha" value="0.1" />