|
1
|
1 <tool id="dwgsim" name="Evaluate simulated reads" version="1.0.0">
|
|
|
2 <description>from a SAM/BAM file using dwgsim_eval</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 if 'sam' == input.ext:
|
|
|
5 dwgsim_wrapper.py \
|
|
|
6 $alignmentScore \
|
|
|
7 $bwa \
|
|
|
8 $colorSpace \
|
|
|
9 -d $scoreFactor \
|
|
|
10 -g $wiggle \
|
|
|
11 -n $numReads \
|
|
|
12 -q $minMapq \
|
|
|
13 $singleEnd \
|
|
|
14 $printIncorrect \
|
|
|
15 -s $numSnps \
|
|
|
16 -e $numErrors \
|
|
|
17 $indels \
|
|
|
18 -s $input \
|
|
|
19 -o $output
|
|
|
20 else:
|
|
|
21 dwgsim_wrapper.py \
|
|
|
22 $alignmentScore \
|
|
|
23 $bwa \
|
|
|
24 $colorSpace \
|
|
|
25 -d $scoreFactor \
|
|
|
26 -g $wiggle \
|
|
|
27 -n $numReads \
|
|
|
28 -q $minMapq \
|
|
|
29 $singleEnd \
|
|
|
30 $printIncorrect \
|
|
|
31 -s $numSnps \
|
|
|
32 -e $numErrors \
|
|
|
33 $indels \
|
|
|
34 -b $input \
|
|
|
35 -o $output
|
|
|
36
|
|
|
37 </command>
|
|
|
38 <inputs>
|
|
|
39 <param format="sam,bam" name="input" type="data" label="SAM/BAM file to evaluate"/>
|
|
|
40 <param name="alignmentScore" type="boolean" truevalue="-a" falsevalue="" checked="False" label="split alignments by alignment score instead of mapping quality"/>
|
|
|
41 <param name="bwa" type="boolean" truevalue="-b" falsevalue="" checked="False" label="alignments are from BWA"/>
|
|
|
42 <param name="colorSpace" type="boolean" truevalue="-c" falsevalue="" checked="False" label="color space alignments"/>
|
|
|
43 <param name="scoreFactor" size="4" type="text" value="1">
|
|
|
44 <label>divide quality/alignment score by this factor</label>
|
|
|
45 </param>
|
|
|
46 <param name="wiggle" size="4" type="text" value="5">
|
|
|
47 <label>gap "wiggle"</label>
|
|
|
48 </param>
|
|
|
49 <param name="numReads" size="4" type="text" value="-1">
|
|
|
50 <label>number of raw input paired-end reads (otherwise, inferred from all SAM records present)</label>
|
|
|
51 </param>
|
|
|
52 <param name="minMapq" size="4" type="text" value="0">
|
|
|
53 <label>consider only alignments with this mapping quality or greater</label>
|
|
|
54 </param>
|
|
|
55 <param name="singleEnd" type="boolean" truevalue="-z" falsevalue="" checked="False" label="input contains only single end reads"/>
|
|
|
56 <param name="printIncorrect" type="boolean" truevalue="-p" falsevalue="" checked="False" label="print incorrect alignments"/>
|
|
|
57 <param name="numSnps" size="4" type="text" value="-1">
|
|
|
58 <label>consider only alignments with the number of specified SNPs</label>
|
|
|
59 </param>
|
|
|
60 <param name="numErrors" size="4" type="text" value="-1">
|
|
|
61 <label>consider only alignments with the number of specified errors</label>
|
|
|
62 </param>
|
|
|
63 <param name="indels" type="boolean" truevalue="-i" falsevalue="" checked="False" label="consider only alignments with indels"/>
|
|
|
64 </inputs>
|
|
|
65 <outputs>
|
|
|
66 <data format="text" name="output"/>
|
|
|
67 </outputs>
|
|
|
68
|
|
|
69 <help>
|
|
|
70 This tool evaluates simulated reads from DWGSIM. For more information, please see https://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation#Evaluating_mapping_-_dwgsim_eval
|
|
|
71 </help>
|
|
|
72
|
|
|
73 </tool>
|
