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comparison repex_full_clustering.xml @ 4:fe2220ee2fd1 draft

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author petr-novak
date Fri, 24 Apr 2020 08:44:45 -0400
parents f99da6158dae
children 335d138b654b
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3:f99da6158dae 4:fe2220ee2fd1
81 <param name="FastaFile" label="NGS reads" type="data" format="fasta" 81 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
82 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/> 82 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
83 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." /> 83 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." />
84 84
85 <conditional name="read_sampling"> 85 <conditional name="read_sampling">
86 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" /> 86 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
87 <when value="false">
88 <!-- pass -->
89 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
90 </when>
87 <when value="true"> 91 <when value="true">
88 <!-- pass --> 92 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
89 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of sequence reads for clustering"/>
90 </when>
91 <when value="false">
92 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of reads for clustering"/>
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95 95
96 96
97 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats"> 97 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
125 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option> 125 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
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">
131 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (search parameters: mgblast, min PID 90, W18) </option> 131 <option value="ILLUMINA" selected="true">Default </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> 132 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
133 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> 133
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> 134 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
135 <option value="OXFORD_NANOPORE" selected="false"> 135 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
136 Pseudo short reads simulated from Oxford Nanopore data, experimental feature! 136 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
137 </option> 137 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
138 <!-- </option> -->
138 </param> 139 </param>
139 </conditional> 140 </conditional>
140 141
141 <conditional name="custom_library"> 142 <conditional name="custom_library">
142 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/> 143 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>