Mercurial > repos > petr-novak > repeatexplorer2
annotate repex_full_clustering.xml @ 7:65d1a27e9339 draft default tip
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
| author | petr-novak |
|---|---|
| date | Mon, 16 Oct 2023 09:19:52 +0000 |
| parents | 335d138b654b |
| children |
| rev | line source |
|---|---|
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" > |
| 0 | 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" /> | |
| 4 <regex match="Traceback" 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" /> | |
| 7 <exit_code range="1:" level="fatal" description="Error" /> | |
| 8 </stdio> | |
| 1 | 9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description> |
| 0 | 10 <requirements> |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container> |
| 0 | 12 </requirements> |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
13 <command> |
| 0 | 14 export PYTHONHASHSEED=0; |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
15 export TAREAN_CPU=\$GALAXY_SLOTS; |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
16 export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB; |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
17 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon |
| 0 | 18 |
| 19 #if $advanced_options.advanced: | |
| 20 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx | |
| 21 --assembly_min $advanced_options.assembly_min_cluster_size | |
| 22 | |
| 23 #if $advanced_options.comparative.options_comparative: | |
| 24 --prefix_length $advanced_options.comparative.prefix_length | |
| 25 #end if | |
| 26 | |
| 27 #if $advanced_options.custom_library.options_custom_library: | |
| 28 -d $advanced_options.custom_library.library extra_database | |
| 29 #end if | |
| 30 | |
| 31 #if $advanced_options.options.options: | |
| 32 -opt $advanced_options.options.options | |
| 33 #end if | |
| 34 #end if | |
| 35 ${FastaFile} >stdout.log 2> stderr.log ; | |
| 36 echo "STDOUT CONTENT:" >> ${log} ; | |
| 37 cat stdout.log >> ${log} ; | |
| 38 echo "STDERR CONTENT:" >> ${log}; | |
| 39 cat stderr.log >> ${log} && | |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
40 /opt/repex_tarean/stderr_filter.py stderr.log && |
| 0 | 41 cd tarean_output && |
| 42 zip -r ${ReportArchive}.zip * && | |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
43 mv ${ReportArchive}.zip ${ReportArchive} && |
| 0 | 44 cp index.html ${ReportFile} && |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
45 mkdir -p ${ReportFile.extra_files_path} && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
46 cp -r --parents libdir ${ReportFile.extra_files_path} && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
48 cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
49 cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
50 cp *.png ${ReportFile.extra_files_path}/ && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
51 cp *.csv ${ReportFile.extra_files_path}/ && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
52 cp *.html ${ReportFile.extra_files_path}/ && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
53 cp *.css ${ReportFile.extra_files_path}/ && |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
54 cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log && rm -r ../tarean_output || : |
| 0 | 55 |
| 56 </command> | |
| 57 <inputs> | |
| 58 <param name="FastaFile" label="NGS reads" type="data" format="fasta" | |
| 1 | 59 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/> |
| 60 <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." /> | |
| 0 | 61 |
| 2 | 62 <conditional name="read_sampling"> |
| 4 | 63 <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" /> |
| 64 <when value="false"> | |
| 2 | 65 <!-- pass --> |
| 4 | 66 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/> |
| 2 | 67 </when> |
| 4 | 68 <when value="true"> |
| 69 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/> | |
| 2 | 70 </when> |
| 71 </conditional> | |
| 72 | |
| 73 | |
| 0 | 74 <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"> |
| 75 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option> | |
| 76 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option> | |
| 77 <option value="METAZOA3.0" >Metazoa version 3.0</option> | |
| 78 <option value="METAZOA2.0" >Metazoa version 2.0</option> | |
| 79 <!-- Modify setting in config.py accordingly --> | |
| 80 </param> | |
| 81 | |
| 82 <conditional name="advanced_options"> | |
| 83 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" /> | |
| 84 <when value="false"> | |
| 85 <!-- pass --> | |
| 86 </when> | |
| 87 <when value="true"> | |
| 88 <conditional name="comparative"> | |
| 1 | 89 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options to analyze multiple samples simultaneously"/> |
| 0 | 90 <when value="false"> |
| 91 <!-- do nothing here --> | |
| 92 </when> | |
| 93 <when value="true"> | |
| 1 | 94 <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, reads from different samples are distinguished by sample codes included as prefix to the read names. See example below."/> |
| 0 | 95 </when> |
| 96 </conditional> | |
| 97 | |
| 98 <conditional name="blastx"> | |
| 99 <param name="options_blastx" type="select" label="Select parameters for protein domain search"> | |
| 100 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option> | |
| 101 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option> | |
| 102 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option> | |
| 103 </param> | |
| 104 </conditional> | |
| 105 | |
| 106 <conditional name="options"> | |
| 4 | 107 <param name="options" type="select" label="Similarity search options"> |
| 108 <option value="ILLUMINA" selected="true">Default </option> | |
| 109 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option> | |
| 110 | |
| 111 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> --> | |
| 112 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> --> | |
| 113 <!-- <option value="OXFORD_NANOPORE" selected="false"> --> | |
| 114 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! --> | |
| 115 <!-- </option> --> | |
| 0 | 116 </param> |
| 117 </conditional> | |
| 118 | |
| 119 <conditional name="custom_library"> | |
| 120 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/> | |
| 121 <when value="false"> | |
| 122 <!-- do nothing here --> | |
| 123 </when> | |
| 124 <when value="true"> | |
| 1 | 125 <param name="library" format="fasta" type="data" label="Custom repeat database" help="The database should contain DNA sequences in FASTA format. The required format for sequence IDs is : '>reapeatname#class/subclass'"/> |
| 0 | 126 </when> |
| 127 </conditional> | |
| 1 | 128 <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; clusters with less than 20 reads are not considered."/> |
| 129 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/> | |
| 130 <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 to keep original names."/> | |
| 131 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/> | |
| 0 | 132 </when> |
| 133 </conditional> | |
|
7
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
134 <param name="queue_select" type="select" label="Select queue"> |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option> |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option> |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option> |
|
65d1a27e9339
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty
petr-novak
parents:
6
diff
changeset
|
138 </param> |
| 0 | 139 |
| 140 </inputs> | |
| 141 <outputs> | |
| 142 <data name="log" format="txt" label="RepeatExplorer2 - log file"/> | |
| 143 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/> | |
| 144 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/> | |
| 145 </outputs> | |
| 146 | |
| 147 <help> | |
| 148 **HELP** | |
| 149 | |
| 150 RepeatExplorer2 clustering is a computational pipeline for unsupervised | |
| 151 identification of repeats from unassembled sequence reads. The | |
| 152 pipeline uses low-pass whole genome sequence reads and performs graph-based | |
| 153 clustering. Resulting clusters, representing all types of repeats, are then | |
| 154 examined to identify and classify into repeats groups. | |
| 155 | |
| 156 **Input data** | |
| 157 | |
| 158 The analysis requires either **single** or **paired-end reads** generated | |
| 159 by whole genome shotgun sequencing provided as a single fasta-formatted file. | |
| 160 Generally, paired-end reads provide significantly better results than single | |
| 161 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and | |
| 162 the number of analyzed reads should represent less than 1x genome equivalent | |
| 163 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be | |
| 164 quality-filtered (recommended filtering : quality score >=10 over 95% of bases | |
| 165 and no Ns allowed) and only **complete read pairs** should be submitted for | |
| 166 analysis. When paired reads are used, input data must be **interlaced** format | |
| 167 as fasta file: | |
| 168 | |
| 169 example of interlaced input format:: | |
| 170 | |
| 171 >0001_f | |
| 172 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG | |
| 173 >0001_r | |
| 174 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT | |
| 175 >0002_f | |
| 176 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG | |
| 177 >0002_r | |
| 178 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC | |
| 179 >0003_f | |
| 180 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT | |
| 181 >0003_r | |
| 182 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT | |
| 183 ... | |
| 184 | |
| 185 | |
| 186 **Comparative analysis** | |
| 187 | |
| 188 For comparative analysis sequence names must contain code (prefix) for each group. | |
| 189 Prefix in sequences names must be of fixed length. | |
| 190 | |
| 191 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB :: | |
| 192 | |
| 193 >AA0001_f | |
| 194 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG | |
| 195 >AA0001_r | |
| 196 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT | |
| 197 >AA0002_f | |
| 198 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG | |
| 199 >AA0002_r | |
| 200 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC | |
| 201 >BB0001_f | |
| 202 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT | |
| 203 >BB0001_r | |
| 204 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT | |
| 205 >BB0002_f | |
| 206 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT | |
| 207 >BB0002_r | |
| 208 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT | |
| 209 | |
| 210 | |
| 211 To prepare quality filtered and interlaced input fasta file from fastq | |
| 212 files, use `Preprocessing of paired-reads`__ tool. | |
| 213 | |
| 214 .. __: tool_runner?tool_id=paired_fastq_filtering | |
| 215 | |
| 216 | |
| 217 **Additional parameters** | |
| 218 | |
| 219 **Sample size** defines how many reads should be used in calculation. | |
| 220 Default setting with 500,000 reads will enable detection of high copy | |
| 221 repeats within several hours of computation time. For higher | |
| 222 sensitivity the sample size can be set higher. Since sample size affects | |
| 223 the memory usage, this parameter may be automatically adjusted to lower | |
| 224 value during the run. Maximum sample size which can be processed depends on | |
| 225 the repetitiveness of analyzed genome. | |
| 226 | |
| 227 | |
| 228 **Select taxon and protein domain database version (REXdb)**. Classification | |
| 229 of transposable elements is based on the similarity to our reference database | |
| 230 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species | |
| 231 can be obtained on `repeatexplorer.org`__. Classification | |
| 232 system used in REXdb is described in article `Systematic survey of plant | |
| 233 LTR-retrotransposons elucidates phylogenetic relationships of their | |
| 234 polyprotein domains and provides a reference for element classification`__ | |
| 235 Database for Metazoa species is still under development so use it with caution. | |
| 236 | |
| 237 .. __: http://repeatexplorer.org | |
| 238 .. __: https://doi.org/10.1186/s13100-018-0144-1 | |
| 239 | |
| 240 **Select parameters for protein domain search** REXdb is compared with s | |
| 241 equence clusters either using blastx or diamond aligner. Diamond program | |
| 242 is about three time faster than blastx with word size 3. | |
| 243 | |
| 244 **Similarity search options** By default sequence reads are compared using | |
| 245 mgblast program. Default threshold is explicitly set to 90% sequence | |
| 246 similarity spanning at least 55% of the read length (in the case of reads | |
| 247 differing in length it applies to the longer one). Additionally, sequence | |
| 248 overlap must be at least 55 nt. If you select option for shorter reads | |
| 249 than 100 nt, minimum overlap 55 nt is not required. | |
| 250 | |
| 251 By default, | |
| 252 mgblast search use DUST program to filter out | |
| 253 low-complexity sequences. If you want | |
| 254 to increase sensitivity of detection of satellites with shorter monomer | |
| 255 use option with '*no masking of low complexity repeats*'. Note that omitting | |
| 256 DUST filtering will significantly increase running times | |
| 257 | |
| 258 | |
| 259 **Automatic filtering of abundant satellite repeats** perform clustering on | |
| 260 smaller dataset of sequence reads to detect abundant high confidence | |
| 261 satellite repeats. If such satellites are detected, sequence reads derived | |
| 262 from these satellites are depleted from input dataset. This step enable more | |
| 263 sensitive detection of less abundant repeats as more reads can be used | |
| 264 in clustering step. | |
| 265 | |
| 266 **Use custom repeat database**. This option allows users to perform similarity | |
| 267 comparison of identified repeats to their custom databases. The repeat class must | |
| 268 be encoded in FASTA headers of database entries in order to allow correct | |
| 269 parsing of similarity hits. Required format for custom database sequence name is: :: | |
| 270 | |
| 271 >reapeatname#class/subclass | |
| 272 | |
| 273 | |
| 274 **Output** | |
| 275 | |
| 276 List of clusters identified as putative satellite repeats, their genomic | |
| 277 abundance and various cluster characteristics. | |
| 278 | |
| 279 Output includes a **HTML summary** with table listing of all analyzed | |
| 280 clusters. More detailed information about clusters is provided in | |
| 281 additional files and directories. All results are also provided as | |
| 282 downloadable **zip archive**. Additionally a **log file** reporting | |
| 283 the progress of the computational pipeline is provided. | |
| 284 | |
| 285 </help> | |
| 286 | |
| 287 </tool> |