Mercurial > repos > iuc > ivar_trim
changeset 16:28e4bcbc86e7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 51d656555f9635bb8988f9eec904ee66657736e1
| author | iuc |
|---|---|
| date | Wed, 19 Apr 2023 08:31:08 +0000 |
| parents | a2b94388d00d |
| children | 0893a1dbb807 |
| files | ivar_trim.xml macros.xml |
| diffstat | 2 files changed, 2 insertions(+), 7 deletions(-) [+] |
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--- a/ivar_trim.xml Sat Mar 25 12:53:12 2023 +0000 +++ b/ivar_trim.xml Wed Apr 19 08:31:08 2023 +0000 @@ -40,12 +40,7 @@ #end if -q $min_qual -s $window_width - ## since v1.4 ivar trim *almost* supports piping its output, but - ## unfortunately still writes *some* regular messages to stdout, - ## so we need to stick writing to an intermediate file for now and - ## want to unify the output stream - -p trimmed 1>&2 && - samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam trimmed.bam + | samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o trimmed.sorted.bam - ]]></command> <inputs> <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
--- a/macros.xml Sat Mar 25 12:53:12 2023 +0000 +++ b/macros.xml Wed Apr 19 08:31:08 2023 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.4.0</token> + <token name="@TOOL_VERSION@">1.4.2</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>