|
23
|
1 <?xml version="1.0"?>
|
|
|
2 <tool id="Softsearch" name="softsearch" version="0.6">
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="0.6">softsearch</requirement>
|
|
|
5 </requirements>
|
|
|
6 <description>for structure variation</description>
|
|
|
7 <command>#if $source.index_source=="history"
|
|
|
8 samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
|
|
|
9 #else
|
|
|
10 samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
|
|
|
11 #end if
|
|
|
12 </command>
|
|
|
13 <inputs>
|
|
|
14 <param name="bam_file" type="data" format="bam" label="BAM Files" />
|
|
|
15 <conditional name="source">
|
|
|
16 <param name="index_source" type="select" label="Choose the source for the reference list">
|
|
|
17 <option value="cached">Locally cached</option>
|
|
|
18 <option value="history">History</option>
|
|
|
19 </param>
|
|
|
20 <when value="history">
|
|
|
21 <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
|
|
|
22 </when>
|
|
|
23 <when value="cached">
|
|
|
24 <param name="ref_fasta" type="select" >
|
|
|
25 <options from_data_table="fasta_indexes">
|
|
|
26 <validator type="no_options" message="No Fasta file is available" />
|
|
|
27 </options>
|
|
|
28 </param>
|
|
|
29 </when>
|
|
|
30 </conditional>
|
|
|
31 <param name="inc" type="hidden" value="n=$RANDOM" />
|
|
|
32 <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" />
|
|
|
33 <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" />
|
|
|
34 <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" />
|
|
|
35 <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" />
|
|
|
36 <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="vcf" name="out_file1" />
|
|
|
40 </outputs>
|
|
|
41 <help>
|
|
|
42 </help>
|
|
|
43 </tool>
|
|
|
44
|
|
|
45
|
|
|
46
|
|
|
47
|
|
|
48
|
|
|
49
|
|
|
50
|
|
|
51
|
|
|
52
|
|
|
53
|
|
|
54
|
|
|
55
|
|
|
56
|
