Mercurial > repos > petr-novak > repeatexplorer2_cerit

comparison repex_full_clustering.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="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.7" > 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" >
2 <stdio> 2 <stdio>
3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> 3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 5 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> 6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
10 <requirements> 10 <requirements>
11 <requirement type="package">last</requirement> 11 <requirement type="package">last</requirement>
12 <requirement type="package">imagemagick</requirement> 12 <requirement type="package">imagemagick</requirement>
13 <requirement type="package">mafft</requirement> 13 <requirement type="package">mafft</requirement>
14 <requirement type="package">blast</requirement> 14 <requirement type="package">blast</requirement>
15 <requirement type="package">diamond</requirement> 15 <requirement type="package" version="0.9.29" >diamond</requirement>
16 <requirement type="package">blast-legacy</requirement> 16 <requirement type="package">blast-legacy</requirement>
17 <requirement type="package">r-igraph</requirement> 17 <requirement type="package">r-igraph</requirement>
18 <requirement type="package">r-data.tree</requirement> 18 <requirement type="package">r-data.tree</requirement>
19 <requirement type="package">r-stringr</requirement> 19 <requirement type="package">r-stringr</requirement>
20 <requirement type="package">r-r2html</requirement> 20 <requirement type="package">r-r2html</requirement>
28 <requirement type="package">r-optparse</requirement> 28 <requirement type="package">r-optparse</requirement>
29 <requirement type="package">r-dbi</requirement> 29 <requirement type="package">r-dbi</requirement>
30 <requirement type="package">r-rsqlite</requirement> 30 <requirement type="package">r-rsqlite</requirement>
31 <requirement type="package">r-rserve</requirement> 31 <requirement type="package">r-rserve</requirement>
32 <requirement type="package">bioconductor-biostrings</requirement> 32 <requirement type="package">bioconductor-biostrings</requirement>
33 <requirement type="package" version="2.3.7">repex_tarean</requirement> 33 <requirement type="package" version="2.3.8">repex_tarean</requirement>
34 <requirement type="set_environment">REPEX</requirement> 34 <requirement type="set_environment">REPEX</requirement>
35 <requirement type="set_environment">REPEX_VERSION</requirement> 35 <requirement type="set_environment">REPEX_VERSION</requirement>
36 <requirement type="package" version="0.9.1" >pyrserve</requirement> 36 <requirement type="package" version="0.9.1" >pyrserve</requirement>
37 </requirements> 37 </requirements>
38 <command > 38 <command >
39 export PYTHONHASHSEED=0; 39 export PYTHONHASHSEED=0;
40 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon 40 \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
41 41
42 #if $advanced_options.advanced: 42 #if $advanced_options.advanced:
43 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx 43 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
44 --assembly_min $advanced_options.assembly_min_cluster_size 44 --assembly_min $advanced_options.assembly_min_cluster_size
45 45
80 <inputs> 80 <inputs>
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 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/> 85 <conditional name="read_sampling">
86 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" />
87 <when value="true">
88 <!-- pass -->
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>
94 </conditional>
95
96
86 <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">
87 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option> 98 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
88 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option> 99 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
89 <option value="METAZOA3.0" >Metazoa version 3.0</option> 100 <option value="METAZOA3.0" >Metazoa version 3.0</option>
90 <option value="METAZOA2.0" >Metazoa version 2.0</option> 101 <option value="METAZOA2.0" >Metazoa version 2.0</option>
115 </param> 126 </param>
116 </conditional> 127 </conditional>
117 128
118 <conditional name="options"> 129 <conditional name="options">
119 <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" help="Different similarity search parameters are used depending on the input data to adjust for differences in read length and error rate">
120 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option> 131 <option value="ILLUMINA" selected="true">Illumina reads, optimized for read length 100 nt or more (search parameters: mgblast, min PID 90, W18) </option>
121 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </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>
122 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> 133 <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option>
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>
123 <option value="OXFORD_NANOPORE" selected="false"> 135 <option value="OXFORD_NANOPORE" selected="false">
124 Pseudo short reads simulated from Oxford Nanopore data (experimental feature) 136 Pseudo short reads simulated from Oxford Nanopore data, experimental feature!
125 </option> 137 </option>
126 </param> 138 </param>
127 </conditional> 139 </conditional>
128 140
129 <conditional name="custom_library"> 141 <conditional name="custom_library">