# HG changeset patch
# User iuc
# Date 1545159892 18000
# Node ID 13b7842c72bca8782d29952bebd10edf8f7ffdee
# Parent  2f097bbdd0b4c319824832a15f08dba9fd1aa4ba
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 6cf009024dfff81b0e0f836b76cf475e7cf84c71

diff -r 2f097bbdd0b4 -r 13b7842c72bc repeatmasker.xml
--- a/repeatmasker.xml	Wed May 23 14:23:57 2018 -0400
+++ b/repeatmasker.xml	Tue Dec 18 14:04:52 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy1" profile="17.01">
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7+galaxy2" profile="17.01">
   <description>RepeatMasker</description>
 
   <requirements>
@@ -6,7 +6,9 @@
   </requirements>
 
   <command detect_errors="exit_code"><![CDATA[
-    RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries &&
+    RM_PATH=\$(which RepeatMasker) && 
+    if [ -z "\$RM_PATH" ] ; then echo "Failed to find RepeatMasker in PATH (\$PATH)" >&2 ; exit 1 ; fi &&
+    RM_LIB_PATH=\$(dirname \$RM_PATH)/../share/RepeatMasker/Libraries &&
     mkdir lib &&
     export REPEATMASKER_LIB_DIR=\$(pwd)/lib &&
       for file in \$(ls \$RM_LIB_PATH) ; do  ln -s \$RM_LIB_PATH/\$file lib/\$file ; done &&
@@ -189,8 +191,8 @@
       <param name="source_type" value="library" />
       <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
       <output name="output_masked_genome" file="small.fasta.masked" />
-      <output name="output_table" file="small.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" />
+      <output name="output_table" file="small.fasta.stats" lines_diff="4" />
+      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
       <output name="output_log" file="small.fasta.log" />
     </test>
     <test expect_num_outputs="7">
@@ -202,8 +204,8 @@
       <param name="poly" value="-poly" />
       <param name="repeat_lib" value="repeats.fasta" ftype="fasta" />
       <output name="output_masked_genome" file="small.fasta.masked" />
-      <output name="output_table" file="small.fasta.stats" lines_diff="4" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" />
+      <output name="output_table" file="small.fasta.stats" lines_diff="6" />
+      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
       <output name="output_log" file="small.fasta.log" />
       <output name="output_alignment" file="small.fasta.align" />
       <output name="output_polymorphic" file="small.fasta.poly" />
@@ -217,7 +219,7 @@
       <param name="species_list" value="anopheles" />
       <output name="output_masked_genome" file="small.fasta.masked" />
       <output name="output_table" file="small_repbase.fasta.stats" lines_diff="2" />
-      <output name="output_repeat_catalog" file="small.fasta.cat" />
+      <output name="output_repeat_catalog" file="small.fasta.cat" lines_diff="2" />
       <output name="output_log" file="small_repbase.fasta.log" />
     </test>
   </tests>