Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 26:e6eba137691f draft

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author petr-novak
date Tue, 05 Nov 2024 13:48:13 +0000
parents adf6673735f7
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25:a27646c27090 26:e6eba137691f
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.11.1" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.12.1" >
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:0.3.11-579a65d</container> 11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.12-7a7dc9e</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));
70 </when> 70 </when>
71 </conditional> 71 </conditional>
72 72
73 73
74 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats"> 74 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
75 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option> 75 <option value="VIRIDIPLANTAE4.0" selected="true">Viridiplantae version 4.0 </option>
76 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option> 76 <option value="VIRIDIPLANTAE3.0" >Viridiplantae version 3.0 </option>
77 <option value="VIRIDIPLANTAE2.2" >Viridiplantae version 2.2</option>
77 <option value="METAZOA3.0" >Metazoa version 3.0</option> 78 <option value="METAZOA3.0" >Metazoa version 3.0</option>
78 <option value="METAZOA2.0" >Metazoa version 2.0</option> 79 <option value="METAZOA2.0" >Metazoa version 2.0</option>
79 <!-- Modify setting in config.py accordingly --> 80 <!-- Modify setting in config.py accordingly -->
80 </param> 81 </param>
81 82