Mercurial > repos > bgruening > racon

annotate racon.xml @ 8:e100a765370e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
author bgruening
date Wed, 19 Oct 2022 16:12:55 +0000
parents d865b62f501c
children 936f0b5e7fcc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
1 <tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
2 <description>Consensus module for raw de novo DNA assembly of long uncorrected reads</description>
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
3 <macros>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
5 </macros>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
6 <expand macro="requirements" />
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
7 <version_command>racon --version</version_command>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
4
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
9 #if $reads.ext.startswith("fasta")
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
10 #set ext="fasta"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
11 #else
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
12 #set ext="fastq"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
13 #end if
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
14 #if $reads.ext.endswith(".gz")
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
15 #set ext=ext+".gz"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
16 #end if
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
17
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
18 ln -s '$reads' reads.$ext &&
1
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
19 #if $overlaps.ext == 'sam':
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
20 ln -s '$overlaps' overlaps.${overlaps.ext} &&
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
21 #else:
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
22 ln -s '$overlaps' overlaps.paf &&
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
23 #end if
4
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
24
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
25 #if $corrected_reads.ext.startswith("fasta")
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
26 #set cext="fasta"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
27 #else
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
28 #set cext="fastq"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
29 #end if
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
30 #if $corrected_reads.ext.endswith(".gz")
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
31 #set cext=cext+".gz"
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
32 #end if
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
33 ln -s '$corrected_reads' corrected_reads.$cext &&
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
34
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
35 racon
4
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
36 reads.$ext
1
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
37 #if $overlaps.ext == 'sam':
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
38 overlaps.${overlaps.ext}
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
39 #else:
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
40 overlaps.paf
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
41 #end if
4
cd06929b224b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"
bgruening
parents: 3
diff changeset
42 corrected_reads.$cext
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
43 -t \${GALAXY_SLOTS:-4}
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
44 $include_unpolished
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
45 $fragment_correction
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
46 -w $window_length
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
47 -q $quality_threshold
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
48 -e $error_threshold
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
49 $no_trimming
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
50 -m $match
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
51 -x $mismatch
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
52 -g $gap
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
53 > racon_polished_consensus.fa
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
54 ]]></command>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
55 <inputs>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
56 <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences" help="input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences used for correction"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
57 <param type="data" name="overlaps" format="paf,sam,tabular" label="Overlaps" help="input file in MHAP/PAF/SAM format (can be compressed with gzip) containing overlaps between sequences and target sequences"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
58 <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences" help="Input file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be corrected"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
59 <param argument="--include-unpolished" type="boolean" truevalue="-u" falsevalue="" label="Include unpolished" help="Output unpolished target sequences" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
60 <param argument="--fragment-correction" type="boolean" truevalue="-f" falsevalue="" label="Fragment correction" help="Perform fragment correction instead of contig polishing. Note: overlaps file should contain dual/self overlaps" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
61 <param argument="--window-length" type="integer" value="500" label="Window length" help="Size of window on which POA is performed"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
62 <param argument="--quality-threshold" type="float" min="0" value="10.0" label="Quality threshold" help="Threshold for average base quality of windows used in POA"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
63 <param argument="--error-threshold" type="float" min="0" value="0.3" label="Error threshold" help="Maximum allowed error rate used for filtering overlaps" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
64 <param argument="--no-trimming" type="boolean" truevalue="--no-trimming" falsevalue="" checked="false" label="No trimming" help="Disables consensus trimming at window ends" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
65 <param argument="--match" type="integer" value="3" label="Match score" help="Score for matching bases. Defalt: 3" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
66 <param argument="--mismatch" type="integer" value="-5" label="Mismatch score" help="Score for mismatching bases. Default: -5" />
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
67 <param argument="--gap" type="integer" value="-4" max="0" label="Gap penalty" />
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
68 </inputs>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
69 <outputs>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
70 <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" label="${tool.name} on ${on_string}: consensus sequence"/>
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
71 </outputs>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
72 <tests>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
73 <test expect_num_outputs="1">
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
74 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
75 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
76 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
77 <param name="include_unpolished" value="true"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
78 <param name="fragment_correction" value="true"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
79 <param name="window_length" value="800"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
80 <param name="error_threshold" value="0.2"/>
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
81 <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
82 </test>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
83 <test expect_num_outputs="1">
1
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
84 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
85 <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
86 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
87 <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
4df02149a270 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a
bgruening
parents: 0
diff changeset
88 </test>
8
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
89 <test expect_num_outputs="1">
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
90 <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
91 <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
92 <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
93 <param name="include_unpolished" value="false"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
94 <param name="fragment_correction" value="false"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
95 <param name="quality_threshold" value="9.0"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
96 <param name="no_trimming" value="true"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
97 <param name="match" value="7"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
98 <param name="mismatch" value="-4"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
99 <param name="gap" value="-3"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
100 <output name="consensus" ftype="fasta" file="consensus_result1.fasta"/>
e100a765370e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit 3ff7b4745ccf85b6cf5a5c64625f9bde6f582b0f
bgruening
parents: 6
diff changeset
101 </test>
0
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
102 </tests>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
103 <help><![CDATA[
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
104
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
105 **What it does**
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
106
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
107 Consensus module for raw de novo DNA assembly of long uncorrected reads.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
108
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
109 Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
110 which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
111 or better quality compared to the output generated by assembly methods which employ both error correction
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
112 and consensus steps, while providing a speedup of several times compared to those methods.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
113 It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
114
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
115 Racon can be used as a polishing tool after the assembly with either Illumina data or data
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
116 produced by third generation of sequencing. The type of data inputed is automatically detected.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
117
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
118 Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
119 format and overlaps/alignments between the reads and the contigs in SAM format. Output is a set of polished contigs in FASTA format printed to stdout.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
120
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
121 Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
122 to contain pairwise overlaps between reads including dual overlaps.
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
123
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
124 ]]></help>
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
125 <expand macro="citations" />
51fd3136069d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203
bgruening
parents:
diff changeset
126 </tool>