Mercurial > repos > iuc > varvamp

comparison macros.xml @ 3:33fac436dd54 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1056d5cc83082613f5d92b22b4e531fa9d505b91
author iuc
date Wed, 08 May 2024 07:05:53 +0000
parents eb5dcbebd242
children 36c91ff33d70
comparison
equal deleted inserted replaced
2:eb5dcbebd242 3:33fac436dd54
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.1.3</token> 3 <token name="@TOOL_VERSION@">1.2.0</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <xml name="main_parameters"> 5 <xml name="main_parameters">
6 <conditional name="main_params"> 6 <conditional name="main_params">
7 <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?"> 7 <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
8 <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option> 8 <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>
51 <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/> 51 <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>
52 </section> 52 </section>
53 <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits"> 53 <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">
54 <param name="BLAST_MAX_DIFF" type="float" min="0" max="1" value="0.5" label="BLAST_MAX_DIFF" help="Minimal fraction of identity to primer to consider a BLAST hit an off-target primer binding site" /> 54 <param name="BLAST_MAX_DIFF" type="float" min="0" max="1" value="0.5" label="BLAST_MAX_DIFF" help="Minimal fraction of identity to primer to consider a BLAST hit an off-target primer binding site" />
55 <param name="BLAST_SIZE_MULTI" type="float" min="1" value="2" label="BLAST_SIZE_MULTI" help="Disregard off-target amplicons with a length greater than the configured maximal length of target amplicons multiplied by this value" /> 55 <param name="BLAST_SIZE_MULTI" type="float" min="1" value="2" label="BLAST_SIZE_MULTI" help="Disregard off-target amplicons with a length greater than the configured maximal length of target amplicons multiplied by this value" />
56 <param name="BLAST_PENALTY" type="integer" min="0" value="50" label="BLAST_PENALTY" help="Extra penalty imposed on amplicons with off-target primer products; the default of 50 should be high enough to consider such amplicons only when no other amplicons without off-target products can be found." />
57 </section> 56 </section>
58 </when> 57 </when>
59 </conditional> 58 </conditional>
60 </when> 59 </when>
61 </conditional> 60 </conditional>