# HG changeset patch
# User iuc
# Date 1609757013 0
# Node ID b72793637686c6d53a6448e9d8e9b7ee82a49280
# Parent  bf328cec6a42c8fd5de2275e8ca59646713f1cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"

diff -r bf328cec6a42 -r b72793637686 samtools_view.xml
--- a/samtools_view.xml	Wed Sep 02 15:29:22 2020 -0400
+++ b/samtools_view.xml	Mon Jan 04 10:43:33 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2">
+<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy3">
     <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
     <macros>
         <import>macros.xml</import>
@@ -43,6 +43,7 @@
     <expand macro="version_command"/>
     <command><![CDATA[
         @ADDTHREADS@
+        @ADDMEMORY@
         ## prepare reference data
         @PREPARE_FASTA_IDX@
         @PREPARE_IDX@
@@ -224,14 +225,14 @@
                 ## then sort the output by coordinate,
                 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
                     && samtools sort
-                        -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+                        -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
                         -O bam
                         -o tmpsam
                         outfile
                         && mv tmpsam outfile
                     #if $with_non_selected_reads_output:
                         && samtools sort
-                            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+                            -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
                             -O bam
                             -o tmpsam
                             inv_outfile