# HG changeset patch
# User iuc
# Date 1566899913 14400
# Node ID 39bde80cd248ab9bcb649c35793d90c165801020
# Parent  41929aa1e7f360af38240e5fe07374093da979a4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"

diff -r 41929aa1e7f3 -r 39bde80cd248 macros.xml
--- a/macros.xml	Sat Aug 17 09:38:21 2019 -0400
+++ b/macros.xml	Tue Aug 27 05:58:33 2019 -0400
@@ -88,7 +88,7 @@
         &&
     #end if
     ]]></token>
-    <token name="@REFGENOMEHANDLING" ><![CDATA[
+    <token name="@REFGENOMEHANDLING@" ><![CDATA[
     --runThreadN \${GALAXY_SLOTS:-4}
     --genomeLoad NoSharedMemory
     --genomeDir
@@ -97,7 +97,7 @@
     #else:
         '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
         ## Handle difference between indices with/without annotations
-        #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
             #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
@@ -114,6 +114,7 @@
             <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
             <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
             <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
+            <yield />
         </stdio>
     </xml>
     <xml name="refgenomehandling" >
@@ -132,10 +133,10 @@
                     </param>
                     <when value="with-gtf">
                         <expand macro="index_selection" with_gene_model="1" />
-                        <expand macro="@SJDBOPTIONS@" />
                     </when>
                     <when value="without-gtf">
                         <expand macro="index_selection" with_gene_model="0" />
+                        <expand macro="@SJDBOPTIONS@" />
                     </when>
                 </conditional>
             </when>
diff -r 41929aa1e7f3 -r 39bde80cd248 test-data/41737_R1.fastq.sub240k.gz
Binary file test-data/41737_R1.fastq.sub240k.gz has changed
diff -r 41929aa1e7f3 -r 39bde80cd248 test-data/41737_R1_sub240k.fastq.gz
Binary file test-data/41737_R1_sub240k.fastq.gz has changed
diff -r 41929aa1e7f3 -r 39bde80cd248 test-data/41737_R2.fastq.sub240k.gz
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diff -r 41929aa1e7f3 -r 39bde80cd248 test-data/41737_R2_sub240k.fastq.gz
Binary file test-data/41737_R2_sub240k.fastq.gz has changed