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comparison softsearch_wrapper.xml @ 14:27a93ada8c7b draft

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author plus91-technologies
date Sat, 07 Jun 2014 04:05:14 -0400
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13:bee54ff79ace 14:27a93ada8c7b
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 | $PATH/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 | $PATH/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>
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