| Previous changeset 8:bf328cec6a42 (2020-09-02) Next changeset 10:350bbc5c2ffd (2021-09-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d" |
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modified:
samtools_view.xml |
| b |
| 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 |