Mercurial > repos > petr-novak > repeatexplorer2_testing
comparison repex_full_clustering.xml @ 18:4308d3e572ee draft
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author | petr-novak |
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date | Thu, 01 Feb 2024 09:43:43 +0000 |
parents | 5cca2c9aa4ad |
children | 19a3d199db8f |
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17:5cca2c9aa4ad | 18:4308d3e572ee |
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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.4" > | 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.9.1" > |
2 <stdio> | 2 <stdio> |
3 <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" /> | 3 <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" /> |
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> | 4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> |
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> | 5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> |
6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> | 6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> |
7 <exit_code range="1:" level="fatal" description="Error" /> | 7 <exit_code range="1:" level="fatal" description="Error" /> |
8 </stdio> | 8 </stdio> |
9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> | 9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> |
10 <requirements> | 10 <requirements> |
11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> | 11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.9-579a65d</container> |
12 </requirements> | 12 </requirements> |
13 <command> | 13 <command> |
14 export PYTHONHASHSEED=0; | 14 export PYTHONHASHSEED=0; |
15 export TAREAN_CPU=\$GALAXY_SLOTS; | 15 export TAREAN_CPU=\$GALAXY_SLOTS; |
16 export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024)); | 16 export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024)); |
17 echo \$GALAXY_MEMORY_MB; | |
18 echo "TAREAN_MAX_MEM=\$TAREAN_MAX_MEM" ; | |
19 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon | 17 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon |
20 | 18 |
21 #if $advanced_options.advanced: | 19 #if $advanced_options.advanced: |
22 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx | 20 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx |
23 --assembly_min $advanced_options.assembly_min_cluster_size | 21 --assembly_min $advanced_options.assembly_min_cluster_size |