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author petr-novak
date Wed, 08 Jan 2020 06:25:59 -0500
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1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.7" >
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>
9 <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description>
10 <requirements>
11 <requirement type="package">last</requirement>
12 <requirement type="package">imagemagick</requirement>
13 <requirement type="package">mafft</requirement>
14 <requirement type="package">blast</requirement>
15 <requirement type="package">diamond</requirement>
16 <requirement type="package">blast-legacy</requirement>
17 <requirement type="package">r-igraph</requirement>
18 <requirement type="package">r-data.tree</requirement>
19 <requirement type="package">r-stringr</requirement>
20 <requirement type="package">r-r2html</requirement>
21 <requirement type="package">r-hwriter</requirement>
22 <requirement type="package">r-dt</requirement>
23 <requirement type="package">r-scales</requirement>
24 <requirement type="package">r-plotrix</requirement>
25 <requirement type="package">r-png</requirement>
26 <requirement type="package">r-plyr</requirement>
27 <requirement type="package">r-dplyr</requirement>
28 <requirement type="package">r-optparse</requirement>
29 <requirement type="package">r-dbi</requirement>
30 <requirement type="package">r-rsqlite</requirement>
31 <requirement type="package">r-rserve</requirement>
32 <requirement type="package">bioconductor-biostrings</requirement>
33 <requirement type="package" version="2.3.7">repex_tarean</requirement>
34 <requirement type="set_environment">REPEX</requirement>
35 <requirement type="set_environment">REPEX_VERSION</requirement>
36 <requirement type="package" version="0.9.1" >pyrserve</requirement>
37 </requirements>
38 <command >
39 export PYTHONHASHSEED=0;
40 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
41
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
44 --assembly_min $advanced_options.assembly_min_cluster_size
45
46 #if $advanced_options.comparative.options_comparative:
47 --prefix_length $advanced_options.comparative.prefix_length
48 #end if
49
50 #if $advanced_options.custom_library.options_custom_library:
51 -d $advanced_options.custom_library.library extra_database
52 #end if
53
54 #if $advanced_options.options.options:
55 -opt $advanced_options.options.options
56 #end if
57 #end if
58 ${FastaFile} >stdout.log 2> stderr.log ;
59 echo "STDOUT CONTENT:" >> ${log} ;
60 cat stdout.log >> ${log} ;
61 echo "STDERR CONTENT:" >> ${log};
62 cat stderr.log >> ${log} &amp;&amp;
63 \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
64 cd tarean_output &amp;&amp;
65 zip -r ${ReportArchive}.zip * &amp;&amp;
66 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
67 cp index.html ${ReportFile} &amp;&amp;
68 mkdir ${ReportFile.files_path} &amp;&amp;
69 cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
70 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
71 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
72 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
73 cp *.png ${ReportFile.files_path}/ &amp;&amp;
74 cp *.csv ${ReportFile.files_path}/ &amp;&amp;
75 cp *.html ${ReportFile.files_path}/ &amp;&amp;
76 cp *.css ${ReportFile.files_path}/ &amp;&amp;
77 cp *.fasta ${ReportFile.files_path}/ 2>>$log &amp;&amp; rm -r ../tarean_output || :
78
79 </command>
80 <inputs>
81 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
82 help="Input file must contain fasta-formatted NGS reads. If paired end reads are used, reads must be interlaced and all pairs must be complete. Example of input data format is provided in the help below. "/>
83 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="Check if you are using pair reads and input sequences contain both read mates and left mates alternate with their right mates" />
84
85 <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
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">
87 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
88 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
89 <option value="METAZOA3.0" >Metazoa version 3.0</option>
90 <option value="METAZOA2.0" >Metazoa version 2.0</option>
91 <!-- Modify setting in config.py accordingly -->
92 </param>
93
94 <conditional name="advanced_options">
95 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
96 <when value="false">
97 <!-- pass -->
98 </when>
99 <when value="true">
100 <conditional name="comparative">
101 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options when you want to compare sequences multiple groups"/>
102 <when value="false">
103 <!-- do nothing here -->
104 </when>
105 <when value="true">
106 <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, sequences are from individial groups distinguished by sample code which must be used as prefix for sequence name. See example below."/>
107 </when>
108 </conditional>
109
110 <conditional name="blastx">
111 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
112 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
113 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
114 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
115 </param>
116 </conditional>
117
118 <conditional name="options">
119 <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">
120 <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
121 <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
122 <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option>
123 <option value="OXFORD_NANOPORE" selected="false">
124 Pseudo short reads simulated from Oxford Nanopore data (experimental feature)
125 </option>
126 </param>
127 </conditional>
128
129 <conditional name="custom_library">
130 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
131 <when value="false">
132 <!-- do nothing here -->
133 </when>
134 <when value="true">
135 <param name="library" format="fasta" type="data" label="Custom library of repeats" help="Library of repeats as DNA sequences in fasta format. The required format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
136 </when>
137 </conditional>
138 <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."/>
139 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering tries to identify the most abundant tandem repeats and remove such sequences partially from analysis. Removal of abundant tandem repeat can enable to analyze higher proportion of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
140 <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."/>
141 <param name="assembly_min_cluster_size" type="integer" label="min cluster size for assembly" value="5" min="2" max="100"/>
142 </when>
143 </conditional>
144
145 <conditional name="queue_definition">
146 <param name="queue_select" type="select" label="Select queue">
147 <option value="basic_fast_queue">basic &amp; fast</option>
148 <option value="long_slow_queue">long &amp; slow</option>
149 <option value="extra_long_slow_queue">extra long &amp; slow</option>
150 </param>
151 <when value="basic_fast_queue">
152 <param name="queue_specification" type="text" label="Modify parameters (optional)"
153 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" />
154 </when>
155
156 <when value="long_slow_queue">
157 <param name="queue_specification" type="text" label="Modify parameters (optional)"
158 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
159 </when>
160 <when value="extra_long_slow_queue">
161 <param name="queue_specification" type="text" label="Modify parameters (optional)"
162 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
163 </when>
164 </conditional>
165
166
167
168 </inputs>
169 <outputs>
170 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
171 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
172 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
173 </outputs>
174
175 <help>
176 **HELP**
177
178 RepeatExplorer2 clustering is a computational pipeline for unsupervised
179 identification of repeats from unassembled sequence reads. The
180 pipeline uses low-pass whole genome sequence reads and performs graph-based
181 clustering. Resulting clusters, representing all types of repeats, are then
182 examined to identify and classify into repeats groups.
183
184 **Input data**
185
186 The analysis requires either **single** or **paired-end reads** generated
187 by whole genome shotgun sequencing provided as a single fasta-formatted file.
188 Generally, paired-end reads provide significantly better results than single
189 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
190 the number of analyzed reads should represent less than 1x genome equivalent
191 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
192 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
193 and no Ns allowed) and only **complete read pairs** should be submitted for
194 analysis. When paired reads are used, input data must be **interlaced** format
195 as fasta file:
196
197 example of interlaced input format::
198
199 >0001_f
200 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
201 >0001_r
202 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
203 >0002_f
204 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
205 >0002_r
206 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
207 >0003_f
208 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
209 >0003_r
210 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
211 ...
212
213
214 **Comparative analysis**
215
216 For comparative analysis sequence names must contain code (prefix) for each group.
217 Prefix in sequences names must be of fixed length.
218
219 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
220
221 >AA0001_f
222 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
223 >AA0001_r
224 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
225 >AA0002_f
226 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
227 >AA0002_r
228 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
229 >BB0001_f
230 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
231 >BB0001_r
232 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
233 >BB0002_f
234 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
235 >BB0002_r
236 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
237
238
239 To prepare quality filtered and interlaced input fasta file from fastq
240 files, use `Preprocessing of paired-reads`__ tool.
241
242 .. __: tool_runner?tool_id=paired_fastq_filtering
243
244
245 **Additional parameters**
246
247 **Sample size** defines how many reads should be used in calculation.
248 Default setting with 500,000 reads will enable detection of high copy
249 repeats within several hours of computation time. For higher
250 sensitivity the sample size can be set higher. Since sample size affects
251 the memory usage, this parameter may be automatically adjusted to lower
252 value during the run. Maximum sample size which can be processed depends on
253 the repetitiveness of analyzed genome.
254
255
256 **Select taxon and protein domain database version (REXdb)**. Classification
257 of transposable elements is based on the similarity to our reference database
258 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
259 can be obtained on `repeatexplorer.org`__. Classification
260 system used in REXdb is described in article `Systematic survey of plant
261 LTR-retrotransposons elucidates phylogenetic relationships of their
262 polyprotein domains and provides a reference for element classification`__
263 Database for Metazoa species is still under development so use it with caution.
264
265 .. __: http://repeatexplorer.org
266 .. __: https://doi.org/10.1186/s13100-018-0144-1
267
268 **Select parameters for protein domain search** REXdb is compared with s
269 equence clusters either using blastx or diamond aligner. Diamond program
270 is about three time faster than blastx with word size 3.
271
272 **Similarity search options** By default sequence reads are compared using
273 mgblast program. Default threshold is explicitly set to 90% sequence
274 similarity spanning at least 55% of the read length (in the case of reads
275 differing in length it applies to the longer one). Additionally, sequence
276 overlap must be at least 55 nt. If you select option for shorter reads
277 than 100 nt, minimum overlap 55 nt is not required.
278
279 By default,
280 mgblast search use DUST program to filter out
281 low-complexity sequences. If you want
282 to increase sensitivity of detection of satellites with shorter monomer
283 use option with '*no masking of low complexity repeats*'. Note that omitting
284 DUST filtering will significantly increase running times
285
286
287 **Automatic filtering of abundant satellite repeats** perform clustering on
288 smaller dataset of sequence reads to detect abundant high confidence
289 satellite repeats. If such satellites are detected, sequence reads derived
290 from these satellites are depleted from input dataset. This step enable more
291 sensitive detection of less abundant repeats as more reads can be used
292 in clustering step.
293
294 **Use custom repeat database**. This option allows users to perform similarity
295 comparison of identified repeats to their custom databases. The repeat class must
296 be encoded in FASTA headers of database entries in order to allow correct
297 parsing of similarity hits. Required format for custom database sequence name is: ::
298
299 >reapeatname#class/subclass
300
301
302 **Output**
303
304 List of clusters identified as putative satellite repeats, their genomic
305 abundance and various cluster characteristics.
306
307 Output includes a **HTML summary** with table listing of all analyzed
308 clusters. More detailed information about clusters is provided in
309 additional files and directories. All results are also provided as
310 downloadable **zip archive**. Additionally a **log file** reporting
311 the progress of the computational pipeline is provided.
312
313 </help>
314
315 </tool>