# HG changeset patch
# User iuc
# Date 1601928846 0
# Node ID e1461b5c52a01a9681e161a4b6f0af4e598f715d
# Parent  65432c3abf6cda1e8d71fe13becbfcc72c16170f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit c1fda24943cf04866d408133ffb6aabf4a90866b"

diff -r 65432c3abf6c -r e1461b5c52a0 lofreq_call.xml
--- a/lofreq_call.xml	Mon Jun 15 13:13:03 2020 -0400
+++ b/lofreq_call.xml	Mon Oct 05 20:14:06 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy0">
+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1" profile="18.01">
     <description>with LoFreq</description>
     <macros>
         <import>macros.xml</import>
@@ -34,11 +34,6 @@
 
         ## call variants with lofreq
 
-        ## make lofreq stick to tool contract by
-        ## generating tmp output inside job working dir
-        mkdir pp-tmp &&
-        export TMPDIR=pp-tmp &&
-
         lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose
 
         --ref '$reference_fasta_fn' --out variants.vcf $variant_types
@@ -96,12 +91,12 @@
 
         ## in case of errors add the log files produced
         ## by the parallel workers to stderr
-        || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code)
+        || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code)
 
         ## work around a bug in lofreq call-parallel
         ## https://github.com/CSB5/lofreq/issues/85
         ## that causes the output format to be vcf.gz with certain filter
-        ## combinations.
+        ## combinations. Issue is closed but still not fixed.
         #if str($bonf_factor) != 'dynamic':
             #if '--no-default-filter' in str($filter_control.others):
                 && ln -s variants.vcf variants.vcf.gz