Mercurial > repos > iuc > hapog
changeset 1:7d56a813fd24 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba
| author | iuc |
|---|---|
| date | Tue, 10 Oct 2023 17:29:42 +0000 |
| parents | c61bc8bb5f1e |
| children | ee0d6e789958 |
| files | hapog.xml test-data/hapog_bam.changes test-data/hapog_short.changes |
| diffstat | 3 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- a/hapog.xml Fri Sep 16 13:48:54 2022 +0000 +++ b/hapog.xml Tue Oct 10 17:29:42 2023 +0000 @@ -1,7 +1,7 @@ <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>genome polishing</description> <macros> - <token name="@TOOL_VERSION@">1.3.3</token> + <token name="@TOOL_VERSION@">1.3.6</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> @@ -12,7 +12,10 @@ --genome '${genome}' --output output/ ---threads \${GALAXY_SLOTS:-1} +## setting default threads to 2 until +## https://github.com/institut-de-genomique/HAPO-G/issues/34 +## gets addressed, at least +--threads \${GALAXY_SLOTS:-2} #if str( $reads.type ) == "short": #for $i in $reads.pe1 @@ -60,8 +63,8 @@ <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" /> </inputs> <outputs> - <data format="fasta" name="output" from_work_dir="output/hapog_results/hapog.fasta"/> - <data format="tsv" name="changes" from_work_dir="output/hapog_results/hapog.changes"/> + <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/> + <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/> </outputs> <tests> <test>
--- a/test-data/hapog_bam.changes Fri Sep 16 13:48:54 2022 +0000 +++ b/test-data/hapog_bam.changes Tue Oct 10 17:29:42 2023 +0000 @@ -1,3 +1,3 @@ NC_0129201 72 ref=A read=G readname=M01368:8:000000000-A3GHV:1:1101:6911:8255 homo ratio1=1.0000 ratio2=1.0000 -NC_0129201 16525 ref=G read=A readname=M01368:8:000000000-A3GHV:1:1104:11928:24197 homo ratio1=0.9758 ratio2=0.9758 +NC_0129201 16525 ref=G read=A readname=M01368:8:000000000-A3GHV:1:1104:11928:24197 homo ratio1=0.9752 ratio2=0.9752
--- a/test-data/hapog_short.changes Fri Sep 16 13:48:54 2022 +0000 +++ b/test-data/hapog_short.changes Tue Oct 10 17:29:42 2023 +0000 @@ -1,3 +1,3 @@ NC_0129201 72 ref=A read=G readname=M01368:8:000000000-A3GHV:1:1101:6911:8255 homo ratio1=1.0000 ratio2=1.0000 -NC_0129201 16525 ref=G read=A readname=M01368:8:000000000-A3GHV:1:1104:11928:24197 homo ratio1=0.9758 ratio2=0.9758 +NC_0129201 16525 ref=G read=A readname=M01368:8:000000000-A3GHV:1:1104:11928:24197 homo ratio1=0.9752 ratio2=0.9752