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comparison varvamp.xml @ 4:36c91ff33d70 draft

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86
author iuc
date Sat, 15 Jun 2024 15:43:28 +0000
parents 33fac436dd54
children d6d746d0d1d0
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3:33fac436dd54 4:36c91ff33d70
177 <param name="QPROBE_GC_RANGE_max" type="integer" min="0" max="100" value="80" label="Maximal qPCR probe GC-content" /> 177 <param name="QPROBE_GC_RANGE_max" type="integer" min="0" max="100" value="80" label="Maximal qPCR probe GC-content" />
178 <param name="QPROBE_GC_RANGE_opt" type="integer" min="0" max="100" value="60" label="Optimal qPCR probe GC-content" /> 178 <param name="QPROBE_GC_RANGE_opt" type="integer" min="0" max="100" value="60" label="Optimal qPCR probe GC-content" />
179 <param name="QPROBE_GC_END_min" type="integer" min="0" max="5" value="0" label="Minimal number of GCs among the 3'-terminal 5 bases of the probe" /> 179 <param name="QPROBE_GC_END_min" type="integer" min="0" max="5" value="0" label="Minimal number of GCs among the 3'-terminal 5 bases of the probe" />
180 <param name="QPROBE_GC_END_max" type="integer" min="0" max="5" value="4" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" /> 180 <param name="QPROBE_GC_END_max" type="integer" min="0" max="5" value="4" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" />
181 <!--constraints for amplicon design--> 181 <!--constraints for amplicon design-->
182 <param name="QPRIMER_DIFF" type="integer" min="0" max="10" value="2" label="Maximal melting temperature difference among qPCR primers" /> 182 <param name="QPRIMER_DIFF" type="integer" min="0" value="2" label="Maximal melting temperature difference among qPCR primers" />
183 <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" max="20" value="5" label="Minimal melting temperature difference between qPCR probe and primers" /> 183 <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />
184 <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" max="20" value="10" label="Maximal melting temperature difference between qPCR probe and primers" /> 184 <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />
185 <param name="QPROBE_DISTANCE_min" type="integer" min="0" max="20" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" /> 185 <param name="QPROBE_DISTANCE_min" type="integer" min="0" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" />
186 <param name="QPROBE_DISTANCE_max" type="integer" min="0" max="20" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" /> 186 <param name="QPROBE_DISTANCE_max" type="integer" min="0" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />
187 <param name="END_OVERLAP" type="integer" min="0" max="10" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" /> 187 <param name="END_OVERLAP" type="integer" min="0" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" />
188 <param name="QAMPLICON_LENGTH_min" type="integer" min="0" max="300" value="70" label="Minimal length of qPCR amplicons" /> 188 <param name="QAMPLICON_LENGTH_min" type="integer" min="0" value="70" label="Minimal length of qPCR amplicons" />
189 <param name="QAMPLICON_LENGTH_max" type="integer" min="0" max="300" value="200" label="Maximal length of qPCR amplicons" /> 189 <param name="QAMPLICON_LENGTH_max" type="integer" min="0" value="200" label="Maximal length of qPCR amplicons" />
190 <param name="QAMPLICON_GC_min" type="integer" min="0" max="100" value="40" label="Minimal GC-content of qPCR amplicons" /> 190 <param name="QAMPLICON_GC_min" type="integer" min="0" max="100" value="40" label="Minimal GC-content of qPCR amplicons" />
191 <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" /> 191 <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" />
192 <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" max="10" value="4" label="Cutoff for deletions allowed in aligned regions under qPCR amplicons" help ="qPCR amplicon candidates are not considered further if they span regions of the alignment that contain deletions as long as this cutoff in bases, or longer."/> 192 <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" value="4" label="Cutoff for deletions allowed in aligned regions under qPCR amplicons" help ="qPCR amplicon candidates are not considered further if they span regions of the alignment that contain deletions as long as this cutoff in bases, or longer."/>
193 </section> 193 </section>
194 </expand> 194 </expand>
195 <expand macro="primer_scheme_outputs"> 195 <expand macro="primer_scheme_outputs">
196 <option value="qpcr_design" selected="true">qPCR amplicon details in tabular format</option> 196 <option value="qpcr_design" selected="true">qPCR amplicon details in tabular format</option>
197 </expand> 197 </expand>