Mercurial > repos > petr-novak > repeatexplorer2
diff repex_tarean.xml @ 3:f99da6158dae draft
Uploaded
author | petr-novak |
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date | Wed, 22 Apr 2020 02:27:53 -0400 |
parents | 09747b55badb |
children | fe2220ee2fd1 |
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--- a/repex_tarean.xml Tue Apr 21 06:39:40 2020 -0400 +++ b/repex_tarean.xml Wed Apr 22 02:27:53 2020 -0400 @@ -109,10 +109,10 @@ <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 if you want to keep original names."/> <conditional name="options"> <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust search to differences in read length and error rate"> - <option value="ILLUMINA" selected="true">Illumina reads, default, all-to-all search uses mgblast, minimal identity 90% </option> - <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> - <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option> - <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option> + <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (parameters: mgblast, min PID 90, W18) </option> + <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats (parameters: mgblast, min PID 90, -W18, -F F) </option> + <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> + <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> </param> </conditional> </when>