Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_tarean.xml @ 19:3d0ba5734776 draft

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Uploaded
author petr-novak
date Thu, 01 Feb 2024 09:44:37 +0000
parents 20ef42e81eeb
children 84106349d4b1
comparison
equal deleted inserted replaced
18:4308d3e572ee 19:3d0ba5734776
1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8.3" > 1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.9.1" >
2 <stdio> 2 <stdio>
3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
4 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 4 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" /> 5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
6 <exit_code range="1:" level="fatal" description="Error" /> 6 <exit_code range="1:" level="fatal" description="Error" />
7 </stdio> 7 </stdio>
8 <description>Identification of genomic tandem repeats from NGS data</description> 8 <description>Identification of genomic tandem repeats from NGS data</description>
9 <requirements> 9 <requirements>
10 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> 10 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.9-579a65d</container>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"> 12 <command detect_errors="exit_code">
13 export PYTHONHASHSEED=0; 13 export PYTHONHASHSEED=0;
14 export TAREAN_CPU=\$GALAXY_SLOTS; 14 export TAREAN_CPU=\$GALAXY_SLOTS;
15 export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB; 15 export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024));
16 seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 16 seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
17 #if $advanced_options.advanced: 17 #if $advanced_options.advanced:
18 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging 18 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
19 #if $advanced_options.custom_library.options_custom_library : 19 #if $advanced_options.custom_library.options_custom_library :
20 -d $advanced_options.custom_library.library extra_database 20 -d $advanced_options.custom_library.library extra_database