Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate repeat_annotate_custom.xml @ 12:755a4d643184 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
author petr-novak
date Tue, 26 Sep 2023 07:28:04 +0000
parents 5366d5ea04bc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
755a4d643184 planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
petr-novak
parents: 11
diff changeset
1 <tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.7" python_template_version="3.5">
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
2 <requirements>
9
4a068d23fda6 Uploaded
petr-novak
parents: 8
diff changeset
3 <requirement type="package" version="4.1.2.p1">repeatmasker</requirement>
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
4 <requirement type="package">bioconductor-rtracklayer</requirement>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
5 </requirements>
11
5366d5ea04bc planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
petr-novak
parents: 10
diff changeset
6 <required_files>
5366d5ea04bc planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
petr-novak
parents: 10
diff changeset
7 <include type="literal" path="clean_rm_output.R"/>
5366d5ea04bc planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
petr-novak
parents: 10
diff changeset
8 </required_files>
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
10
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
11 #if $sensitivity.value == 'default':
8
2557cad81607 Uploaded
petr-novak
parents: 7
diff changeset
12 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
13 #else:
8
2557cad81607 Uploaded
petr-novak
parents: 7
diff changeset
14 RepeatMasker -dir \$(pwd) '$input' -pa 32 -lib '$repeat_library' -xsmall ${nolow} -no_is -e ncbi $sensitivity
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
15 #end if
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
16 &&
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
17 ls -l * >&2 &&
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
18 cp `basename $input`.out $output2
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
19 &&
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
20 Rscript ${__tool_directory__}/clean_rm_output.R $output2 $output1
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
21
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
22 ]]></command>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
23 <inputs>
7
acf12f2e8355 "planemo upload commit 363c9be36812ce7623dad670f881d155209ed2ba"
petr-novak
parents: 6
diff changeset
24 <param type="data" name="input" format="fasta" label="Genome assembly to annotate" />
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
25 <param type="data" name="repeat_library" format="fasta" label="RepeatExplorer based Library of Repetitive Sequences"
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
26 help="custom database of repetitive sequences should be provided in fasta format. Sequence header should specify repeat class:
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
27 >sequence_id#classification_level1/classification_level2/..." />
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
28 <param type="select" label="sensitivity" name="sensitivity" >
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
29 <option value="default" selected="true" >Default sensitivity </option>
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
30 <option value="-s">Slow search, more sensitive </option>
6
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents: 4
diff changeset
31 <option value="-q">Quick search, less sensitive </option>
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
32 </param>
12
755a4d643184 planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
petr-novak
parents: 11
diff changeset
33 <param argument="-nolow" type="boolean" truevalue="" falsevalue="-nolow" checked="true" label="Perform masking of low complexity and simple repeats" />
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
34 </inputs>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
35 <outputs>
6
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents: 4
diff changeset
36 <data name="output1" format="gff3" label="Repeat Annotation (GFF3) on ${on_string}"/>
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
37 <data name="output2" format="tabular" label="Raw output from RepeatMasker on ${on_string}" />
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
38 </outputs>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
39 <help><![CDATA[
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
40 This tools uses RepeatMasker to annotate repetitive sequences in the genome assemblies using custom library of repeats created either from RepeatExplorer output or from DANTE_LTR transposable element library.
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
41 Library of repeats can be created from RepeatExplorer output from contigs and TAREAN consensus sequences.
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
42 Fasta formatted library of repeats must contain header containing information about classification of repeats as **>sequence_id#classification_level1/classification_level2/...**
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
43
3
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
44 Classification in RepeatExplorer based library follows predetermined classification levels. User can however specify additional classification levels or custom classifications.
4ea506b39297 "planemo upload"
petr-novak
parents: 2
diff changeset
45 Conflicts in annotations are resolved based on classification hierarchy.
0
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
46 ]]></help>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
47 </tool>
ea6a3059a6af Uploaded
petr-novak
parents:
diff changeset
48