Mercurial > repos > bgruening > tgsgapcloser

annotate tgsgapcloser.xml @ 0:86fa46d3ce2e 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/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
author bgruening
date Sun, 14 Nov 2021 21:28:36 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
1 <tool id="tgsgapcloser" name="TGS-GapCloser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
2 <description>fills the N-gap of error-prone long reads</description>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
3 <macros>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
5 </macros>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
6 <expand macro="requirements" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
7 <expand macro="xrefs"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
8 <version_command>tgsgapcloser --version</version_command>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
10 PILON=\$(which pilon)
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
11 PILON_JAR=\$(readlink -f \$PILON).jar
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
12 && tgsgapcloser
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
13 --scaff $scaff
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
14 --reads $reads
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
15 --output output
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
16 #if $error_conditional.error_options == 'pilon'
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
17 --pilon \$PILON_JAR
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
18 --ngs $error_conditional.ngs
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
19 --samtools `which samtools`
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
20 --java `which java`
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
21 --pilon_mem \${GALAXY_MEMORY_MB:-4096}M
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
22 #elif $error_conditional.error_options == 'racon'
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
23 --racon `which racon`
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
24 #else
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
25 --ne
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
26 #end if
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
27 --tgstype $tgstype_conditional.tgstype
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
28 --min_idy $tgstype_conditional.min_idy
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
29 --min_match $tgstype_conditional.min_match
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
30 --chunk $chunk
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
31 $g_check
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
32 --thread \${GALAXY_SLOTS:-16}
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
33 ]]></command>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
34 <inputs>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
35 <param argument="--scaff" type="data" format="fasta" multiple="true" label="Scaffold file" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
36 <param argument="--reads" type="data" format="fasta" multiple="true" label="Input reads" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
37 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
38 <param name="error_options" type="select" label="Error correction">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
39 <option value="ne">Do not error correct</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
40 <option value="racon">Racon</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
41 <option value="pilon">Pilon</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
42 </param>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
43 <when value="ne"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
44 <when value="racon">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
45 <param argument="--r_round" type="integer" min="0" max="10" value="1" label="Number of Racon error-correction rounds"
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
46 help="Although multiple rounds of racon can increase the quality of an assembly there are indications that it also
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
47 fragments the assembly and may decrease quality by removing structural variants and SNPs. Published assembly workflows
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
48 differ in the number of rounds but rarely apply more than 4 rounds of racon" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
49 </when>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
50 <when value="pilon">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
51 <param argument="--ngs" type="data" format="fastq,fastq.gz" label="Illumina reads"
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
52 help="Pilon can utilize Illumina short reads mapped to the draft assembly to
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
53 improve the local accuracy of the sequence by correcting sequence errors,
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
54 fixing misassemblies, and filling gaps"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
55 <param argument="--p_round" type="integer" min="0" max="10" value="3" label="Number of Pilon error-correction rounds" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
56 </when>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
57 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
58 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
59 <param argument="--tgstype" type="select" label="Type of third generation reads">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
60 <option value="ont" selected="true">Oxford Nanopore Technologies (ONT)</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
61 <option value="pb">PacBio (pb)</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
62 </param>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
63 <when value="ont">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
64 <param argument="--min_idy" type="float" min="0" max="1" value="0.3" label="Minimum identity for filtering candidate sequences"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
65 <param argument="--min_match" type="integer" min="0" max="1000" value="300" label="Minimum matched length for filtering candidate sequences"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
66 </when>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
67 <when value="pb">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
68 <param argument="--min_idy" type="float" min="0" max="1" value="0.2" label="Minimum identity for filtering candidate sequences"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
69 <param argument="--min_match" type="integer" min="0" max="1000" value="200" label="Minimum matched length for filtering candidate sequences"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
70 </when>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
71 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
72 <param argument="--chunk" type="integer" min="0" max="20" value="3" label="Chunks for error correction" help="Split candidates into # of chunks to separately correct errors" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
73 <param argument="--g_check" type="boolean" truevalue="--g_check" falsevalue="" label="Gap-size diff check"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
74 <param name="output_options" type="select" multiple="true" optional="true" display="checkboxes" label="Output files">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
75 <option value="log_file">General log file</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
76 <option value="gapfill_log">Gapfill log file</option>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
77 </param>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
78 </inputs>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
79 <outputs>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
80 <data name="log" format="txt" from_work_dir="output.fill.log" label="${tool.name} on ${on_string}: log">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
81 <filter>output_options and 'log_file' in output_options</filter>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
82 </data>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
83 <data name="final_assembly" format="fasta" from_work_dir="output.scaff_seqs" label="${tool.name} on ${on_string}: final assembly"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
84
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
85 <data name="fill_details" format="txt" from_work_dir="output.gap_fill_detail" label="${tool.name} on ${on_string}: gap fill details">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
86 <filter>output_options and 'gapfill_log' in output_options</filter>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
87 </data>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
88 </outputs>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
89 <tests>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
90 <!--Test 01: no correction-->
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
91 <test expect_num_outputs="3">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
92 <param name="scaff" value="scaffold.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
93 <param name="reads" value="ont_reads.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
94 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
95 <param name="error_options" value="ne"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
96 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
97 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
98 <param name="tgstype" value="ont"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
99 <param name="min_idy" value="0.3"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
100 <param name="min_match" value="300"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
101 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
102 <param name="chunk" value="3"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
103 <param name="g_check" value="false"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
104 <param name="output_options" value="log_file,gapfill_log"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
105 <output name="final_assembly" file="test_01_final_assembly.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
106 <output name="log" ftype="txt">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
107 <assert_contents>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
108 <has_text text="TGSGapCloser start now"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
109 <has_text text="the one read provide filler choose count freq for a gap"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
110 </assert_contents>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
111 </output>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
112 <output name="fill_details" file="test_01_gapfill.log" ftype="txt"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
113 </test>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
114 <!--Test 02: correction with racon-->
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
115 <test expect_num_outputs="1">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
116 <param name="scaff" value="scaffold.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
117 <param name="reads" value="ont_reads.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
118 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
119 <param name="error_options" value="racon"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
120 <param name="r_round" value="2"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
121 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
122 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
123 <param name="tgstype" value="ont"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
124 <param name="min_idy" value="0.3"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
125 <param name="min_match" value="300"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
126 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
127 <param name="chunk" value="3"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
128 <param name="g_check" value="false"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
129 <output name="final_assembly" file="test_02_final_assembly.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
130 </test>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
131 <!--Test 03: correction pilon-->
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
132 <test expect_num_outputs="1">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
133 <param name="scaff" value="scaffold.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
134 <param name="reads" value="ont_reads.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
135 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
136 <param name="error_options" value="pilon"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
137 <param name="ngs" value="ngs_reads.fastq" ftype="fastq"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
138 <param name="r_round" value="1"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
139 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
140 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
141 <param name="tgstype" value="ont"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
142 <param name="min_idy" value="0"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
143 <param name="min_match" value="0"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
144 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
145 <param name="chunk" value="1"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
146 <param name="g_check" value="true"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
147 <output name="final_assembly" file="test_03_final_assembly.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
148 </test>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
149 <!--Test 04: correction with racon and pacbio-->
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
150 <test expect_num_outputs="1">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
151 <param name="scaff" value="scaffold.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
152 <param name="reads" value="ont_reads.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
153 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
154 <param name="error_options" value="racon"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
155 <param name="r_round" value="2"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
156 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
157 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
158 <param name="tgstype" value="pacbio"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
159 <param name="min_idy" value="0.2"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
160 <param name="min_match" value="200"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
161 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
162 <param name="chunk" value="2"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
163 <param name="g_check" value="false"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
164 <output name="final_assembly" file="test_04_final_assembly.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
165 </test>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
166 <!--Test 05: fastq.gz files-->
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
167 <test expect_num_outputs="1">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
168 <param name="scaff" value="scaffold.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
169 <param name="reads" value="ont_reads.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
170 <conditional name="error_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
171 <param name="error_options" value="pilon"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
172 <param name="ngs" value="ngs_reads.fastq.gz" ftype="fastq.gz"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
173 <param name="r_round" value="1"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
174 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
175 <conditional name="tgstype_conditional">
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
176 <param name="tgstype" value="ont"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
177 <param name="min_idy" value="0"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
178 <param name="min_match" value="0"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
179 </conditional>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
180 <param name="chunk" value="1"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
181 <param name="g_check" value="false"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
182 <output name="final_assembly" file="test_05_final_assembly.fasta" ftype="fasta"/>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
183 </test>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
184 </tests>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
185 <help><![CDATA[
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
186
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
187 .. class:: infomark
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
188
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
189 **Purpose**
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
190
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
191 TGS-GapCloser is a gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio,
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
192 Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly. This tool can close gaps in large genome assemblies
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
193 using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
194 completeness while maintaining high accuracy.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
195
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
196 ----
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
197
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
198 .. class:: infomark
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
199
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
200 **Quick usage**
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
201
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
202 Input reads can only be in FASTA format. Both raw reads and pre-error-corrected reads are acceptable as input. If only raw long reads are
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
203 provided, it polishes raw TGS reads by calling Racon.If additional NGS short reads are available, it polishes raw TGS reads by calling Pilon.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
204
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
205 ----
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
206
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
207 .. class:: infomark
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
208
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
209 **Gap fill details**
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
210
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
211
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
212 Format of a detailed information of gap fill report:
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
213
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
214 - Each scaffold name is followed by its data lines.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
215 - A data line consists of 3 or 5 columns and describes the source of each segment in the final sequence:
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
216 - Column 1 is the segment's first bp position in the final sequence.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
217 - Column 2 is the segment's last bp position in the final sequence.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
218 - Column 3 is the segment's type , 'S' , 'N' or 'F'.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
219 - 'S' means this segment is a segment of the input sequence and this line includes other two more columns:
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
220 - Column 4 is the segment's first bp position in the input sequence.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
221 - Column 5 is the segment's last bp position in the input sequence.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
222 - 'N' means this segment is a N area.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
223 - 'F' means this segment is a filled sequence from TGS reads.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
224
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
225 ----
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
226
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
227 .. class:: infomark
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
228
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
229 **Algorithm and implementation of TGS-GapCloser**
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
230
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
231 This is a brief description of the TGS-GapCloser algorithm. Please refer to the manuscript for more detailed information.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
232
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
233 TGS-GapCloser is coded in the C++ programing language (requires GCC 4.4+). It uses minimap2 to obtain alignments, and Pilon (requires Java runtime 1.7+)
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
234 or Racon (requires GCC 4.8+) to correct candidate fragments. The algorithm automatically identifies gaps and tries to find the best matched long-read
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
235 fragments to close gaps or merge adjacent scaftigs. To accelerate the gap closure without losing efficiency and accuracy, TGS-GapCloser only selects a
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
236 limited number of fragmented long reads as candidates for subsequent error correction and competition.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
237
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
238 TGS-GapCloser can accept as input any type of TGS long reads or other pre-assembled contigs to fill gaps in a draft assembly in the 4 steps :
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
239 (i) Identification of gap regions in the draft assembly;
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
240 (ii) Acquisition of candidates from the alignments of long reads against gaps;
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
241 (iii) Base-level error correction of alternative sub-long reads; and
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
242 (iv) Gap closure using the error-corrected candidates with the highest score for each gap or linkage of the neighboring scaftigs with overlaps.
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
243
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
244 ]]></help>
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
245 <expand macro="citations" />
86fa46d3ce2e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser commit dcc6bd722244004ed2d5ac49d53a4e1d71366b1a"
bgruening
parents:
diff changeset
246 </tool>