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comparison repex_tarean.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
107 <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/> 107 <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
108 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/> 108 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
109 <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."/> 109 <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."/>
110 <conditional name="options"> 110 <conditional name="options">
111 <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"> 111 <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">
112 <option value="ILLUMINA" selected="true">Illumina reads, default, all-to-all search uses mgblast, minimal identity 90% </option> 112 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (parameters: mgblast, min PID 90, W18) </option>
113 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> 113 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats (parameters: mgblast, min PID 90, -W18, -F F) </option>
114 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option> 114 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option>
115 <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option> 115 <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option>
116 </param> 116 </param>
117 </conditional> 117 </conditional>
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 120