Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_tarean.xml @ 6:4b3af335dca8 draft

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author petr-novak
date Wed, 14 Apr 2021 06:20:12 +0000
parents 397394c00bf7
children ffe53359f758
comparison
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5:397394c00bf7 6:4b3af335dca8
1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8" > 1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2." >
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">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container> 10 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</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 seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 14 seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
15 #if $advanced_options.advanced: 15 #if $advanced_options.advanced: