Mercurial > repos > gga > repeatexplorer_clustering

annotate repex_full_clustering.xml @ 0:6eec21828dd4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
author gga
date Thu, 02 Nov 2023 16:20:35 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
1 <tool id="repeatexplorer_clustering" name="RepeatExplorer (clustering)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
2 <description>repeat discovery and characterization using graph-based sequence clustering</description>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
3 <macros>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
4 <import>macros.xml</import>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
5 </macros>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
6 <expand macro="creator"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
7 <expand macro="requirements"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
8 <command><![CDATA[
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
9
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
10 export GALAXY_MEMORY_KB=\$((\${GALAXY_MEMORY_MB:-8192}*1024))
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
11 &&
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
12
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
13 export PYTHONHASHSEED=0
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
14 &&
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
15
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
16 ## output will go here
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
17 mkdir -p '${reportfile.extra_files_path}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
18 &&
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
19
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
20 /repex_tarean/seqclust
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
21 --cpu \${GALAXY_SLOTS:-1}
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
22 --max_memory \${GALAXY_MEMORY_KB}
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
23 '${paired}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
24 #if $sample:
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
25 --sample '${sample}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
26 #end if
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
27 --taxon '${taxon}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
28 --output_dir='${reportfile.extra_files_path}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
29 #if $advanced.mincl:
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
30 --mincl '${advanced.mincl}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
31 #end if
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
32 --assembly_min '${advanced.assembly_min}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
33 #if $advanced.keep_names:
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
34 --keep_names
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
35 #end if
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
36 '${fastafile}'
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
37 &&
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
38
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
39 ## pick up the html index
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
40 cp '${reportfile.extra_files_path}/index.html' ./index.html
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
41
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
42 ]]></command>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
43 <inputs>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
44 <param name="fastafile" label="NGS reads" type="data" format="fasta" help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
45 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, they must be interleaved and all pairs must be complete. Example of the correct format is provided in the help below."/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
46 <param argument="--sample" type="integer" min="2" optional="true" label="Subsample reads (number)" help="Use an integer &gt; 1 to select a specific number of reads to use. Leave this field blank to use the entire dataset."/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
47 <param argument="--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">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
48 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0</option>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
49 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
50 <option value="METAZOA3.0">Metazoa version 3.0</option>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
51 <option value="METAZOA2.0">Metazoa version 2.0</option>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
52 </param>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
53 <section name="advanced" title="Advanced options" expanded="false">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
54 <param argument="--mincl" label="Cluster size threshold for detailed analysis" type="float" value="" min="0.0001" max="100" optional="true" help="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; clusters with less than 20 reads are not considered."/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
55 <param argument="--assembly_min" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
56 <param argument="--keep_names" label="Keep original read names" type="boolean" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
57 </section>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
58 </inputs>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
59 <outputs>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
60 <data name="reportfile" format="html" from_work_dir="index.html" label="RepeatExplorer - HTML report on ${on_string}"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
61 </outputs>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
62 <tests>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
63 <!-- test1: basic function -->
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
64 <test expect_num_outputs="1">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
65 <param name="fastafile" value="LAS_paired_10k.fa.gz" ftype="fasta.gz"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
66 <param name="paired" value="True"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
67 <param name="taxon" value="VIRIDIPLANTAE3.0"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
68 <output name="reportfile">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
69 <assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
70 <has_text text="Clustering summary"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
71 </assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
72 </output>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
73 </test>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
74 <!-- test2: read subsample -->
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
75 <test expect_num_outputs="1">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
76 <param name="fastafile" value="LAS_paired_10k.fa.gz" ftype="fasta.gz"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
77 <param name="paired" value="True"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
78 <param name="sample" value="5000"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
79 <param name="taxon" value="VIRIDIPLANTAE3.0"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
80 <output name="reportfile">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
81 <assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
82 <has_text text="Clustering summary"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
83 </assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
84 </output>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
85 </test>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
86 <!-- test3: advanced params -->
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
87 <test expect_num_outputs="1">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
88 <param name="fastafile" value="LAS_paired_10k.fa.gz" ftype="fasta.gz"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
89 <param name="paired" value="True"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
90 <param name="taxon" value="VIRIDIPLANTAE3.0"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
91 <param name="mincl" value="0.01"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
92 <param name="keep_names" value="True"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
93 <output name="reportfile">
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
94 <assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
95 <has_text text="Clustering summary"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
96 </assert_contents>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
97 </output>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
98 </test>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
99 </tests>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
100 <help><![CDATA[
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
101 **HELP**
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
102
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
103 RepeatExplorer2 clustering is a computational pipeline for unsupervised
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
104 identification of repeats from unassembled sequence reads. The
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
105 pipeline uses low-pass whole genome sequence reads and performs graph-based
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
106 clustering. Resulting clusters, representing all types of repeats, are then
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
107 examined to identify and classify into repeats groups.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
108
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
109 **Input data**
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
110
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
111 The analysis requires either **single** or **paired-end reads** generated
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
112 by whole genome shotgun sequencing provided as a single fasta-formatted file.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
113 Generally, paired-end reads provide significantly better results than single
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
114 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
115 the number of analyzed reads should represent less than 1x genome equivalent
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
116 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
117 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
118 and no Ns allowed) and only **complete read pairs** should be submitted for
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
119 analysis. When paired reads are used, input data must be **interlaced** format
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
120 as fasta file:
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
121
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
122 example of interlaced input format::
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
123
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
124 >0001_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
125 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
126 >0001_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
127 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
128 >0002_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
129 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
130 >0002_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
131 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
132 >0003_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
133 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
134 >0003_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
135 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
136 ...
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
137
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
138
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
139 **Comparative analysis**
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
140
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
141 For comparative analysis sequence names must contain code (prefix) for each group.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
142 Prefix in sequences names must be of fixed length.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
143
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
144 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
145
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
146 >AA0001_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
147 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
148 >AA0001_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
149 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
150 >AA0002_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
151 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
152 >AA0002_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
153 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
154 >BB0001_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
155 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
156 >BB0001_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
157 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
158 >BB0002_f
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
159 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
160 >BB0002_r
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
161 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
162
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
163
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
164 To prepare quality filtered and interlaced input fasta file from fastq
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
165 files, use `Preprocessing of paired-reads`__ tool.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
166
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
167 .. __: tool_runner?tool_id=paired_fastq_filtering
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
168
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
169
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
170 **Additional parameters**
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
171
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
172 **Sample size** defines how many reads should be used in calculation.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
173 Default setting with 500,000 reads will enable detection of high copy
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
174 repeats within several hours of computation time. For higher
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
175 sensitivity the sample size can be set higher. Since sample size affects
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
176 the memory usage, this parameter may be automatically adjusted to lower
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
177 value during the run. Maximum sample size which can be processed depends on
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
178 the repetitiveness of analyzed genome.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
179
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
180
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
181 **Select taxon and protein domain database version (REXdb)**. Classification
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
182 of transposable elements is based on the similarity to our reference database
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
183 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
184 can be obtained on `repeatexplorer.org`__. Classification
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
185 system used in REXdb is described in article `Systematic survey of plant
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
186 LTR-retrotransposons elucidates phylogenetic relationships of their
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
187 polyprotein domains and provides a reference for element classification`__
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
188 Database for Metazoa species is still under development so use it with caution.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
189
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
190 .. __: http://repeatexplorer.org
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
191 .. __: https://doi.org/10.1186/s13100-018-0144-1
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
192
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
193 **Select parameters for protein domain search** REXdb is compared with s
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
194 equence clusters either using blastx or diamond aligner. Diamond program
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
195 is about three time faster than blastx with word size 3.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
196
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
197 **Similarity search options** By default sequence reads are compared using
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
198 mgblast program. Default threshold is explicitly set to 90% sequence
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
199 similarity spanning at least 55% of the read length (in the case of reads
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
200 differing in length it applies to the longer one). Additionally, sequence
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
201 overlap must be at least 55 nt. If you select option for shorter reads
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
202 than 100 nt, minimum overlap 55 nt is not required.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
203
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
204 By default,
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
205 mgblast search use DUST program to filter out
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
206 low-complexity sequences. If you want
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
207 to increase sensitivity of detection of satellites with shorter monomer
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
208 use option with '*no masking of low complexity repeats*'. Note that omitting
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
209 DUST filtering will significantly increase running times
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
210
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
211
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
212 **Automatic filtering of abundant satellite repeats** perform clustering on
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
213 smaller dataset of sequence reads to detect abundant high confidence
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
214 satellite repeats. If such satellites are detected, sequence reads derived
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
215 from these satellites are depleted from input dataset. This step enable more
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
216 sensitive detection of less abundant repeats as more reads can be used
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
217 in clustering step.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
218
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
219 **Use custom repeat database**. This option allows users to perform similarity
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
220 comparison of identified repeats to their custom databases. The repeat class must
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
221 be encoded in FASTA headers of database entries in order to allow correct
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
222 parsing of similarity hits. Required format for custom database sequence name is: ::
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
223
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
224 >reapeatname#class/subclass
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
225
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
226
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
227 **Output**
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
228
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
229 List of clusters identified as putative satellite repeats, their genomic
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
230 abundance and various cluster characteristics.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
231
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
232 Output includes a **HTML summary** with table listing of all analyzed
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
233 clusters. More detailed information about clusters is provided in
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
234 additional files and directories. All results are also provided as
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
235 downloadable **zip archive**. Additionally a **log file** reporting
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
236 the progress of the computational pipeline is provided.
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
237
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
238 ]]></help>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
239 <expand macro="citations"/>
6eec21828dd4 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 commit 3407a4e6a60ff89a0ab5eab87ab94b0d9a209500
gga
parents:
diff changeset
240 </tool>