# HG changeset patch
# User matthias
# Date 1561474512 14400
# Node ID cda59db1b4ee45b71a95f3e6f37cadc7bdf831b1
# Parent  742c94cfb8cfb00605a908cb0406dcc4501038b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3

diff -r 742c94cfb8cf -r cda59db1b4ee macros.xml
--- a/macros.xml	Thu Jun 20 08:10:32 2019 -0400
+++ b/macros.xml	Tue Jun 25 10:55:12 2019 -0400
@@ -107,12 +107,12 @@
     <!-- log file handling -->
     <token name="@TEE_APPEND_LOG@"><![CDATA[
         #if $output_log
-            2>> $output_log &&
+            2>> '$output_log' &&
         #end if
     ]]></token>
     <token name="@CAT_LOG_TO_STDERR@"><![CDATA[
         #if $output_log
-            cat $output_log 2>&1
+            cat '$output_log' 2>&1
         #end if
     ]]></token>
     <xml name="in_log">
@@ -216,11 +216,15 @@
         </expand>
     </xml>
 
-    <!-- fastq input (used in denovomap, tsv2bam, ustacks) -->
-    <xml name="fastq_input" token_fastq_optional="false" token_help="">
+    <!-- fastq input (used in denovomap, tsv2bam, ustacks) 
+         - fastq_optional: makes fastq input optional (true/false) 
+         - se_option: wording for "single end" option (for tsv2bam this is the
+              reverse reads for the others its the forward reads)
+         - help: help text -->
+    <xml name="fastq_input" token_fastq_optional="false" token_se_option="single end or forward reads" token_help="">
         <conditional name="input_type">
             <param name="input_type_select" type="select" label="Short read data from individuals" help="@HELP@">
-                <option value="single" selected="true">single end or forward reads</option>
+                <option value="single" selected="true">@SE_OPTION@</option>
                 <option value="paired">(paired) dataset list</option>
             </param>
             <when value="single">
diff -r 742c94cfb8cf -r cda59db1b4ee test-data/.gentest.sh.swp
Binary file test-data/.gentest.sh.swp has changed