Mercurial > repos > petr-novak > repeatexplorer2_cerit
comparison repex_tarean.xml @ 4:d89d4fa8a17b draft
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author | petr-novak |
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date | Fri, 24 Apr 2020 08:48:32 -0400 |
parents | 67964b619af8 |
children | ed5a72d4693d |
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3:67964b619af8 | 4:d89d4fa8a17b |
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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"> |