Mercurial > repos > petr-novak > repeatexplorer2
diff repex_full_clustering.xml @ 7:65d1a27e9339 draft default tip
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
| author | petr-novak |
|---|---|
| date | Mon, 16 Oct 2023 09:19:52 +0000 |
| parents | 335d138b654b |
| children |
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--- a/repex_full_clustering.xml Fri May 27 12:00:40 2022 +0000 +++ b/repex_full_clustering.xml Mon Oct 16 09:19:52 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.1" > +<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" > <stdio> <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> @@ -8,36 +8,13 @@ </stdio> <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> <requirements> - <requirement type="package">last</requirement> - <requirement type="package">imagemagick</requirement> - <requirement type="package">mafft</requirement> - <requirement type="package">blast</requirement> - <requirement type="package" version="0.9.29" >diamond</requirement> - <requirement type="package">blast-legacy</requirement> - <requirement type="package">r-igraph</requirement> - <requirement type="package">r-data.tree</requirement> - <requirement type="package">r-stringr</requirement> - <requirement type="package">r-r2html</requirement> - <requirement type="package">r-hwriter</requirement> - <requirement type="package">r-dt</requirement> - <requirement type="package">r-scales</requirement> - <requirement type="package">r-plotrix</requirement> - <requirement type="package">r-png</requirement> - <requirement type="package">r-plyr</requirement> - <requirement type="package">r-dplyr</requirement> - <requirement type="package">r-optparse</requirement> - <requirement type="package">r-dbi</requirement> - <requirement type="package">r-rsqlite</requirement> - <requirement type="package">r-rserve</requirement> - <requirement type="package">bioconductor-biostrings</requirement> - <requirement type="package" version="2.3.8.1">repex_tarean</requirement> - <requirement type="set_environment">REPEX</requirement> - <requirement type="set_environment">REPEX_VERSION</requirement> - <requirement type="package" version="0.9.1" >pyrserve</requirement> + <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> </requirements> - <command > +<command> export PYTHONHASHSEED=0; - \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon + export TAREAN_CPU=\$GALAXY_SLOTS; + export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB; + seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx @@ -60,21 +37,21 @@ cat stdout.log >> ${log} ; echo "STDERR CONTENT:" >> ${log}; cat stderr.log >> ${log} && - \${REPEX}/stderr_filter.py stderr.log && + /opt/repex_tarean/stderr_filter.py stderr.log && cd tarean_output && zip -r ${ReportArchive}.zip * && - mv ${ReportArchive}.zip ${ReportArchive} && + mv ${ReportArchive}.zip ${ReportArchive} && cp index.html ${ReportFile} && - mkdir ${ReportFile.files_path} && - cp -r --parents libdir ${ReportFile.files_path} && - cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} && - cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} && - cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls && - cp *.png ${ReportFile.files_path}/ && - cp *.csv ${ReportFile.files_path}/ && - cp *.html ${ReportFile.files_path}/ && - cp *.css ${ReportFile.files_path}/ && - cp *.fasta ${ReportFile.files_path}/ 2>>$log && rm -r ../tarean_output || : + mkdir -p ${ReportFile.extra_files_path} && + cp -r --parents libdir ${ReportFile.extra_files_path} && + cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} && + cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} && + cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls && + cp *.png ${ReportFile.extra_files_path}/ && + cp *.csv ${ReportFile.extra_files_path}/ && + cp *.html ${ReportFile.extra_files_path}/ && + cp *.css ${ReportFile.extra_files_path}/ && + cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log && rm -r ../tarean_output || : </command> <inputs> @@ -154,8 +131,11 @@ <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/> </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>