Mercurial > repos > iuc > samtools_view
changeset 9:be7c8e8a5d08 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
| author | iuc |
|---|---|
| date | Mon, 04 Jan 2021 10:42:59 +0000 |
| parents | a8d747577392 |
| children | 0b341e4e6ec1 |
| files | samtools_view.xml |
| diffstat | 1 files changed, 4 insertions(+), 3 deletions(-) [+] |
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--- a/samtools_view.xml Wed Sep 02 19:28:45 2020 +0000 +++ b/samtools_view.xml Mon Jan 04 10:42:59 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