Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 14:ba67036e6b3c draft

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author petr-novak
date Mon, 16 Oct 2023 09:22:12 +0000
parents 1eefa5b3e8b9
children 15185fe48bf8
comparison
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13:1eefa5b3e8b9 14:ba67036e6b3c
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.1" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" >
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" />
10 <requirements> 10 <requirements>
11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> 11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
12 </requirements> 12 </requirements>
13 <command> 13 <command>
14 export PYTHONHASHSEED=0; 14 export PYTHONHASHSEED=0;
15 export TAREAN_CPU=\$GALAXY_SLOTS;
16 export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB;
15 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon 17 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
16 18
17 #if $advanced_options.advanced: 19 #if $advanced_options.advanced:
18 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx 20 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
19 --assembly_min $advanced_options.assembly_min_cluster_size 21 --assembly_min $advanced_options.assembly_min_cluster_size
127 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/> 129 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
128 <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/> 130 <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
129 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/> 131 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
130 </when> 132 </when>
131 </conditional> 133 </conditional>
132 134 <param name="queue_select" type="select" label="Select queue">
133 <conditional name="queue_definition"> 135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
134 <param name="queue_select" type="select" label="Select queue"> 136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> 137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> 138 </param>
137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
138 </param>
139 <when value="basic_fast_queue">
140 <param name="queue_specification" type="text" label="Modify parameters (optional)"
141 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
142 </when>
143
144 <when value="long_slow_queue">
145 <param name="queue_specification" type="text" label="Modify parameters (optional)"
146 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
147 </when>
148 <when value="extra_long_slow_queue">
149 <param name="queue_specification" type="text" label="Modify parameters (optional)"
150 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
151 </when>
152 </conditional>
153
154
155 139
156 </inputs> 140 </inputs>
157 <outputs> 141 <outputs>
158 <data name="log" format="txt" label="RepeatExplorer2 - log file"/> 142 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
159 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/> 143 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>