Mercurial > repos > petr-novak > repeatexplorer2_cerit

comparison repex_tarean.xml @ 4:d89d4fa8a17b draft

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author petr-novak
date Fri, 24 Apr 2020 08:48:32 -0400
parents 67964b619af8
children ed5a72d4693d
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3:67964b619af8 4:d89d4fa8a17b
74 74
75 <inputs> 75 <inputs>
76 <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta" 76 <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
77 help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/> 77 help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
78 78
79 <conditional name="read_sampling"> 79 <conditional name="read_sampling">
80 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" /> 80 <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" />
81 <when value="false">
82 <!-- pass -->
83 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
84 </when>
81 <when value="true"> 85 <when value="true">
82 <!-- pass --> 86 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
83 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of sequence reads for clustering"/>
84 </when>
85 <when value="false">
86 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of reads for clustering"/>
87 </when> 87 </when>
88 </conditional> 88 </conditional>
89
90 89
91 <conditional name="advanced_options"> 90 <conditional name="advanced_options">
92 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" /> 91 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
93 <when value="false"> 92 <when value="false">
94 <!-- pass --> 93 <!-- pass -->
105 </when> 104 </when>
106 </conditional> 105 </conditional>
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."/> 106 <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"/> 107 <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."/> 108 <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"> 109 <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"> 110 <param name="options" type="select" label="Similarity search options">
112 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (parameters: mgblast, min PID 90, W18) </option> 111 <option value="ILLUMINA" selected="true">Default </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> 112 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
114 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> 113
115 <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> 114 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
116 </param> 115 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
117 </conditional> 116 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
117 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
118 <!-- </option> -->
119 </param>
120 </conditional>
118 </when> 121 </when>
119 </conditional> 122 </conditional>
120 123
121 <conditional name="queue_definition"> 124 <conditional name="queue_definition">
122 <param name="queue_select" type="select" label="Select queue"> 125 <param name="queue_select" type="select" label="Select queue">