Mercurial > repos > petr-novak > repeatexplorer2_testing

comparison repex_full_clustering.xml @ 5:397394c00bf7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petr-novak
date Fri, 09 Apr 2021 08:09:53 +0000
parents 72c028e3e70e
children 4b3af335dca8
comparison
equal deleted inserted replaced
4:72c028e3e70e 5:397394c00bf7
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."/> 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."/>
129 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/> 129 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
130 </when> 130 </when>
131 </conditional> 131 </conditional>
132 132
133 133 <conditional name="queue_definition">
134 <param name="queue_select" type="select" label="Select queue">
135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
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
134 155
135 </inputs> 156 </inputs>
136 <outputs> 157 <outputs>
137 <data name="log" format="txt" label="RepeatExplorer2 - log file"/> 158 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
138 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/> 159 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>