Mercurial > repos > devteam > bowtie2
changeset 26:09b2cdb7ace5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
| author | iuc |
|---|---|
| date | Tue, 12 Jan 2021 16:58:26 +0000 |
| parents | 749c918495f7 |
| children | a6d65b0c67af |
| files | bowtie2_macros.xml bowtie2_wrapper.xml |
| diffstat | 2 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/bowtie2_macros.xml Fri Aug 23 13:24:25 2019 -0400 +++ b/bowtie2_macros.xml Tue Jan 12 16:58:26 2021 +0000 @@ -1,4 +1,5 @@ <macros> + <token name="@TOOL_VERSION@">2.4.2</token> <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@">
--- a/bowtie2_wrapper.xml Fri Aug 23 13:24:25 2019 -0400 +++ b/bowtie2_wrapper.xml Tue Jan 12 16:58:26 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01"> +<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> </macros> <requirements> - <requirement type="package" version="2.3.4.1">bowtie2</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement> + <requirement type="package" version="1.11">samtools</requirement> </requirements> <version_command>bowtie2 --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -305,7 +305,7 @@ ## output file #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): - | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output' + | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' #else if $sam_options.reorder: | samtools view -bS - -o '$output' #else: