Mercurial > repos > petr-novak > repeatrxplorer

comparison repex_full_clustering.xml @ 2:394a697ffa49 draft

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Uploaded
author petr-novak
date Mon, 06 Jan 2020 03:59:39 -0500
parents 1d1b9e1b2e2f
children ee6fbf1bf166
comparison
equal deleted inserted replaced
1:54897aa887fe 2:394a697ffa49
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " > 1 <tool id="repeatexplorer2x" name="RepeatExplorer2 clustering: " version="2.3.6" >
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" />
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 <requirement type="package" version="3.7">python</requirement> 11 <requirement type="package" version="3.7">python</requirement>
12 <requirement type="package" version="0.9.1" >pyrserve</requirement> 12 <requirement type="package" version="0.9.1" >pyrserve</requirement>
13 <requirement type="package">last</requirement>
13 <requirement type="package">mafft</requirement> 14 <requirement type="package">mafft</requirement>
14 <requirement type="package">imagemagick</requirement> 15 <requirement type="package">imagemagick</requirement>
15 <requirement type="package">blast</requirement> 16 <requirement type="package">blast</requirement>
16 <requirement type="package">diamond</requirement> 17 <requirement type="package">diamond</requirement>
17 <requirement type="package">blast-legacy</requirement> 18 <requirement type="package">blast-legacy</requirement>
29 <requirement type="package">r-optparse</requirement> 30 <requirement type="package">r-optparse</requirement>
30 <requirement type="package">r-dbi</requirement> 31 <requirement type="package">r-dbi</requirement>
31 <requirement type="package">r-rsqlite</requirement> 32 <requirement type="package">r-rsqlite</requirement>
32 <requirement type="package">r-rserve</requirement> 33 <requirement type="package">r-rserve</requirement>
33 <requirement type="package">bioconductor-biostrings</requirement> 34 <requirement type="package">bioconductor-biostrings</requirement>
35 <requirement type="package" version="1.0">repex_tarean</requirement>
36 <requirement type="set_environment">REPEX</requirement>
34 </requirements> 37 </requirements>
35 <command > 38 <command >
36 export PYTHONHASHSEED=0; 39 export PYTHONHASHSEED=0;
37 ${__tool_directory__}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon 40 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
38 41
39 #if $advanced_options.advanced: 42 #if $advanced_options.advanced:
40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx 43 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
41 --assembly_min $advanced_options.assembly_min_cluster_size 44 --assembly_min $advanced_options.assembly_min_cluster_size
42 45