Mercurial > repos > petr-novak > repeatexplorer2_testing
changeset 16:20ef42e81eeb draft
Uploaded
| author | petr-novak |
|---|---|
| date | Wed, 20 Dec 2023 14:25:46 +0000 |
| parents | 15185fe48bf8 |
| children | 5cca2c9aa4ad |
| files | repex_tarean.xml |
| diffstat | 1 files changed, 9 insertions(+), 24 deletions(-) [+] |
line wrap: on
line diff
--- a/repex_tarean.xml Wed Dec 20 14:24:48 2023 +0000 +++ b/repex_tarean.xml Wed Dec 20 14:25:46 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8.1" > +<tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8.3" > <stdio> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> <regex match="error" source="stderr" level="fatal" description="Unknown error" /> @@ -11,6 +11,8 @@ </requirements> <command detect_errors="exit_code"> export PYTHONHASHSEED=0; + export TAREAN_CPU=\$GALAXY_SLOTS; + export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB; seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging @@ -56,7 +58,7 @@ <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" /> <when value="false"> <!-- pass --> - <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/> + <param name="sample" label="Sample size" type="hidden" value="0" help="Number of analyzed reads"/> </when> <when value="true"> <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/> @@ -97,28 +99,11 @@ </when> </conditional> - <conditional name="queue_definition"> - <param name="queue_select" type="select" label="Select queue"> - <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> - <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> - <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> - </param> - <when value="basic_fast_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" /> - </when> - - <when value="long_slow_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> - </when> - <when value="extra_long_slow_queue"> - <param name="queue_specification" type="text" label="Modify parameters (optional)" - value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" /> - </when> - </conditional> - - + <param name="queue_select" type="select" label="Select queue"> + <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> + <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> + <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> + </param> </inputs> <outputs>