# HG changeset patch
# User matthias
# Date 1561474728 14400
# Node ID 2626e58c493e6e6cd778aa8d3e7e6e85d50e946d
# Parent  852044374da15a42d2583995e2ab8788694d5130
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3

diff -r 852044374da1 -r 2626e58c493e macros.xml
--- a/macros.xml	Thu Jun 20 08:13:59 2019 -0400
+++ b/macros.xml	Tue Jun 25 10:58:48 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 852044374da1 -r 2626e58c493e stacks_tsv2bam.xml
--- a/stacks_tsv2bam.xml	Thu Jun 20 08:13:59 2019 -0400
+++ b/stacks_tsv2bam.xml	Tue Jun 25 10:58:48 2019 -0400
@@ -54,7 +54,7 @@
         <expand macro="input_cat_macro"/>
         <expand macro="input_matches_macro"/>
         <!-- TODO add BAM? -->
-        <expand macro="fastq_input" fastq_optional="true" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam"/>
+        <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>
         <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
         <expand macro="in_log"/>
     </inputs>
diff -r 852044374da1 -r 2626e58c493e test-data/.gentest.sh.swp
Binary file test-data/.gentest.sh.swp has changed