Mercurial > repos > petr-novak > repeatexplorer2_cerit

comparison repex_tarean.xml @ 3:67964b619af8 draft

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author petr-novak
date Wed, 22 Apr 2020 02:29:47 -0400
parents 968f0867acc5
children d89d4fa8a17b
comparison
equal deleted inserted replaced
2:968f0867acc5 3:67964b619af8
1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.7" > 1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8" >
2 <stdio> 2 <stdio>
3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
4 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 4 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" /> 5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
6 <exit_code range="1:" level="fatal" description="Error" /> 6 <exit_code range="1:" level="fatal" description="Error" />
8 <description>Identification of genomic tandem repeats from NGS data</description> 8 <description>Identification of genomic tandem repeats from NGS data</description>
9 <requirements> 9 <requirements>
10 <requirement type="package">imagemagick</requirement> 10 <requirement type="package">imagemagick</requirement>
11 <requirement type="package">mafft</requirement> 11 <requirement type="package">mafft</requirement>
12 <requirement type="package">blast</requirement> 12 <requirement type="package">blast</requirement>
13 <requirement type="package">diamond</requirement> 13 <requirement type="package" version="0.9.29">diamond</requirement>
14 <requirement type="package">blast-legacy</requirement> 14 <requirement type="package">blast-legacy</requirement>
15 <requirement type="package">r-igraph</requirement> 15 <requirement type="package">r-igraph</requirement>
16 <requirement type="package">r-data.tree</requirement> 16 <requirement type="package">r-data.tree</requirement>
17 <requirement type="package">r-stringr</requirement> 17 <requirement type="package">r-stringr</requirement>
18 <requirement type="package">r-r2html</requirement> 18 <requirement type="package">r-r2html</requirement>
26 <requirement type="package">r-optparse</requirement> 26 <requirement type="package">r-optparse</requirement>
27 <requirement type="package">r-dbi</requirement> 27 <requirement type="package">r-dbi</requirement>
28 <requirement type="package">r-rsqlite</requirement> 28 <requirement type="package">r-rsqlite</requirement>
29 <requirement type="package">r-rserve</requirement> 29 <requirement type="package">r-rserve</requirement>
30 <requirement type="package">bioconductor-biostrings</requirement> 30 <requirement type="package">bioconductor-biostrings</requirement>
31 <requirement type="package" version="2.3.7">repex_tarean</requirement> 31 <requirement type="package" version="2.3.8">repex_tarean</requirement>
32 <requirement type="set_environment">REPEX</requirement> 32 <requirement type="set_environment">REPEX</requirement>
33 <requirement type="set_environment">REPEX_VERSION</requirement> 33 <requirement type="set_environment">REPEX_VERSION</requirement>
34 <requirement type="package" version="0.9.1">pyrserve</requirement> 34 <requirement type="package" version="0.9.1">pyrserve</requirement>
35 </requirements> 35 </requirements>
36 <command detect_errors="exit_code"> 36 <command detect_errors="exit_code">
37 export PYTHONHASHSEED=0; 37 export PYTHONHASHSEED=0;
38 \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode 38 \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
39 #if $advanced_options.advanced: 39 #if $advanced_options.advanced:
40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging 40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
41 #if $advanced_options.custom_library.options_custom_library : 41 #if $advanced_options.custom_library.options_custom_library :
42 -d $advanced_options.custom_library.library extra_database 42 -d $advanced_options.custom_library.library extra_database
43 #end if 43 #end if
73 </command> 73 </command>
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 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/> 78
79 <conditional name="read_sampling">
80 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" />
81 <when value="true">
82 <!-- pass -->
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>
88 </conditional>
89
79 90
80 <conditional name="advanced_options"> 91 <conditional name="advanced_options">
81 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" /> 92 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
82 <when value="false"> 93 <when value="false">
83 <!-- pass --> 94 <!-- pass -->
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."/> 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."/>
97 <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"/>
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."/> 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."/>
99 <conditional name="options"> 110 <conditional name="options">
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"> 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">
101 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option> 112 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (parameters: mgblast, min PID 90, W18) </option>
102 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </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>
103 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </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">Illumina reads, more sensitive search (parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option>
104 </param> 116 </param>
105 </conditional> 117 </conditional>
106 </when> 118 </when>
107 </conditional> 119 </conditional>
108 120