Mercurial > repos > petr-novak > repeatexplorer2_cerit

comparison repex_tarean.xml @ 2:968f0867acc5 draft

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documentation and help update
author petr-novak
date Mon, 03 Feb 2020 02:34:46 -0500
parents e2b8e71b85b9
children 67964b619af8
comparison
equal deleted inserted replaced
1:e6fb0f2b2097 2:968f0867acc5
71 71
72 72
73 </command> 73 </command>
74 74
75 <inputs> 75 <inputs>
76 <param name="FastaFile" label="paired-end NGS 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 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 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/> 78 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
79 79
80 <conditional name="advanced_options"> 80 <conditional name="advanced_options">
81 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" /> 81 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
82 <when value="false"> 82 <when value="false">
91 </when> 91 </when>
92 <when value="true"> 92 <when value="true">
93 <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/> 93 <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
94 </when> 94 </when>
95 </conditional> 95 </conditional>
96 <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 at all."/> 96 <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."/>
97 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/> 97 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
98 <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using integers. If you want to keep original names, use this option."/> 98 <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."/>
99 <conditional name="options"> 99 <conditional name="options">
100 <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate"> 100 <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">
101 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option> 101 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
102 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option> 102 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
103 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> 103 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option>
104 </param> 104 </param>
105 </conditional> 105 </conditional>
106 </when> 106 </when>
107 </conditional> 107 </conditional>
108 108
109 <conditional name="queue_definition"> 109 <conditional name="queue_definition">
110 <param name="queue_select" type="select" label="Select queue"> 110 <param name="queue_select" type="select" label="Select queue">
111 <option value="basic_fast_queue">basic &amp; fast</option> 111 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
112 <option value="long_slow_queue">long &amp; slow</option> 112 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
113 <option value="extra_long_slow_queue">extra long &amp; slow</option> 113 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
114 </param> 114 </param>
115 <when value="basic_fast_queue"> 115 <when value="basic_fast_queue">
116 <param name="queue_specification" type="text" label="Modify parameters (optional)" 116 <param name="queue_specification" type="text" label="Modify parameters (optional)"
117 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" /> 117 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
118 </when> 118 </when>