Mercurial > repos > petr-novak > repeatrxplorer

comparison repex_tarean.xml @ 3:c0ae68651c11 draft

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Uploaded
author petr-novak
date Mon, 06 Jan 2020 04:00:31 -0500
parents 1d1b9e1b2e2f
children ee202a87eecc
comparison
equal deleted inserted replaced
2:394a697ffa49 3:c0ae68651c11
1 <tool id="tarean" name="Tandem Repeat Analyzer" > 1 <tool id="tareanx" name="Tandem Repeat Analyzer" version="2.3.6" >
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 <requirement type="package" version="3.7">python</requirement> 10 <requirement type="package" version="3.7">python</requirement>
11 <requirement type="package" version="0.9.1" >pyrserve</requirement> 11 <requirement type="package" version="0.9.1" >pyrserve</requirement>
12 <requirement type="package">last</requirement>
12 <requirement type="package">mafft</requirement> 13 <requirement type="package">mafft</requirement>
13 <requirement type="package">imagemagick</requirement> 14 <requirement type="package">imagemagick</requirement>
14 <requirement type="package">blast</requirement> 15 <requirement type="package">blast</requirement>
15 <requirement type="package">diamond</requirement> 16 <requirement type="package">diamond</requirement>
16 <requirement type="package">blast-legacy</requirement> 17 <requirement type="package">blast-legacy</requirement>
28 <requirement type="package">r-optparse</requirement> 29 <requirement type="package">r-optparse</requirement>
29 <requirement type="package">r-dbi</requirement> 30 <requirement type="package">r-dbi</requirement>
30 <requirement type="package">r-rsqlite</requirement> 31 <requirement type="package">r-rsqlite</requirement>
31 <requirement type="package">r-rserve</requirement> 32 <requirement type="package">r-rserve</requirement>
32 <requirement type="package">bioconductor-biostrings</requirement> 33 <requirement type="package">bioconductor-biostrings</requirement>
34 <requirement type="package" version="1.0">repex_tarean</requirement>
35 <requirement type="set_environment">REPEX</requirement>
33 </requirements> 36 </requirements>
34
35 <command detect_errors="exit_code"> 37 <command detect_errors="exit_code">
36 export PYTHONHASHSEED=0; 38 export PYTHONHASHSEED=0;
37 ${__tool_directory__}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 39 \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
38 #if $advanced_options.advanced: 40 #if $advanced_options.advanced:
39 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging 41 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
40 #if $advanced_options.custom_library.options_custom_library : 42 #if $advanced_options.custom_library.options_custom_library :
41 -d $advanced_options.custom_library.library extra_database 43 -d $advanced_options.custom_library.library extra_database
42 #end if 44 #end if