Mercurial > repos > petr-novak > repeatexplorer2

comparison repex_full_clustering.xml @ 3:f99da6158dae draft

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author petr-novak
date Wed, 22 Apr 2020 02:27:53 -0400
parents 09747b55badb
children fe2220ee2fd1
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2:09747b55badb 3:f99da6158dae
126 </param> 126 </param>
127 </conditional> 127 </conditional>
128 128
129 <conditional name="options"> 129 <conditional name="options">
130 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust for differences in read length and error rate"> 130 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust for differences in read length and error rate">
131 <option value="ILLUMINA" selected="true">Illumina reads, default, all-to-all search uses mgblast, minimal identity 90% </option> 131 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (search parameters: mgblast, min PID 90, W18) </option>
132 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> 132 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats (search parameters: mgblast, min PID 90, -W18, -F F) </option>
133 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option> 133 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option>
134 <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option> 134 <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option>
135 <option value="OXFORD_NANOPORE" selected="false"> 135 <option value="OXFORD_NANOPORE" selected="false">
136 Pseudo short reads simulated from Oxford Nanopore data, experimental feature! 136 Pseudo short reads simulated from Oxford Nanopore data, experimental feature!
137 </option> 137 </option>
138 </param> 138 </param>
139 </conditional> 139 </conditional>