Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 18:4308d3e572ee draft

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author petr-novak
date Thu, 01 Feb 2024 09:43:43 +0000
parents 5cca2c9aa4ad
children 19a3d199db8f
comparison
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17:5cca2c9aa4ad 18:4308d3e572ee
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