Mercurial > repos > bgruening > lighter

comparison lighter.xml @ 0:89b453176d05 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
author bgruening
date Sat, 04 Jun 2016 12:38:34 -0400
parents
children b0cfd92907eb
comparison
equal deleted inserted replaced
-1:000000000000 0:89b453176d05
1 <tool id="lighter" name="lighter" version="1.0" profile="16.04">
2 <description>can correct the reads containing sequence errors</description>
3 <requirements>
4 <requirement type="package" version="1.1.1">lighter</requirement>
5 </requirements>
6 <command><![CDATA[
7 lighter
8 #for $file in $r:
9 -r $file
10 #end for
11 #if str($kmer.k_select) == "smallk":
12 -k $kmer.k_parameter_string
13 #elif str($kmer.k_select) == "bigK":
14 -K $kmer.K_parameter_string
15 #end if
16 -od ./
17 -t \${GALAXY_SLOTS:-4}
18 #if $maxcor:
19 -maxcor $maxcor
20 #end if
21 $trim
22 $discard
23 $noQual
24 #if $newQual:
25 -newQual '$newQual'
26 #end if
27 $stable
28 > $outfile
29 ]]>
30 </command>
31 <inputs>
32 <param argument="-r" multiple="True" type="data" label="Input file"/>
33 <conditional name="kmer">
34 <param name="k_select" type="select" label="Do you want k or K?">
35 <option value="smallk">small k</option>
36 <option value="bigK">big K</option>
37 </param>
38 <when value="smallk">
39 <param name="k_parameter_string" size="30" type="text" value="13 20 0.2" label="type in 3 parameters"
40 help="(—k kmer_length genome_size alpha)" />
41 </when>
42 <when value="bigK">
43 <param name="K_parameter_string" size="30" type="text" value="13 20" label="type in 2 parameters"
44 help="(—K kmer_length genome_size)" />
45 </when>
46 </conditional>
47 <param argument="-maxcor" type="integer" value="4" optional="True"
48 label="Maximum number of correction for within a kmer length window" help=""/>
49 <param argument="-trim" type="boolean" truevalue="-trim" falsevalue="" checked="False"
50 label="Whether or not to allow trimming"/>
51 <param argument="-discard" type="boolean" truevalue="-discard" falsevalue="" checked="False"
52 label="Whether or not to discard unfixable reads. Will lose paired-end matching when discarding"/>
53 <param argument="-noQual" type="boolean" truevalue="-noQual" falsevalue="" checked="False"
54 label="Whether or not to ignore the quality socre"/>
55 <param argument="-newQual" size="30" type="text" value="" optional="True"
56 label="Quality for the bases corrected to the specified score" help="" />
57 <param argument="-stable" type="boolean" truevalue="-stable" falsevalue="" checked="False"
58 label="Sequentialize the sampling stage, output the same result with different runs"/>
59 </inputs>
60 <outputs>
61 <data name="outfile" format_source="r"/>
62 </outputs>
63 <tests>
64 <test>
65 <param name="r" value="bwa-mem-fastq1.fq"/>
66 <param name="k_select" value="smallk"/>
67 <param name="newQual" value="12 12 0.1"/>
68 <param name="noQual" value="True"/>
69 <param name="stable" value="False"/>
70 <output name="outfile" file="lighter_result1.fq"/>
71 </test>
72 <test>
73 <param name="r" value="bwa-mem-fastq1.fq"/>
74 <param name="k_select" value="bigK"/>
75 <param name="newQual" value="20 14"/>
76 <param name="noQual" value="False"/>
77 <param name="stable" value="True"/>
78 <output name="outfile" file="lighter_result2.fq"/>
79 </test>
80 </tests>
81 <help>
82 **What it does**
83
84 Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling
85 (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information,
86 Lighter can correct the reads containing sequence errors.
87
88 <citations>
89 <citation type="doi">10.1186/s13059-014-0509-9</citation>
90 </citations>
91 </help>
92 </tool>