Mercurial > repos > plus91-technologies-pvt-ltd > softsearch

comparison softsearch.xml @ 22:06581c4fe59f draft

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author plus91-technologies-pvt-ltd
date Wed, 04 Jun 2014 10:02:25 -0400
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21:cdb3daae984a 22:06581c4fe59f
1 <?xml version="1.0"?>
2 <tool id="SoftSearch" name="SoftSearch">
3 <description>for structure variation</description>
4 <command>#if $source.index_source=="history"
5 samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | /home/plus91/2.4/src/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
6 #else
7 samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | /home/plus91/2.4/src//2.4/src/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 $out_file1
8 #end if
9 </command>
10 <inputs>
11 <param name="bam_file" type="data" format="bam" label="BAM Files" />
12 <conditional name="source">
13 <param name="index_source" type="select" label="Choose the source for the reference list">
14 <option value="cached">Locally cached</option>
15 <option value="history">History</option>
16 </param>
17 <when value="history">
18 <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
19 </when>
20 <when value="cached">
21 <param name="ref_fasta" type="select" >
22 <options from_data_table="fasta_indexes">
23 <validator type="no_options" message="No Fasta file is available" />
24 </options>
25 </param>
26 </when>
27 </conditional>
28 <param name="inc" type="hidden" value="n=$RANDOM" />
29 <param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" />
30 <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" />
31 <param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" />
32 <param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" />
33 <param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />
34 </inputs>
35 <outputs>
36 <data format="vcf" name="out_file1" />
37 </outputs>
38 <help>
39 </help>
40 </tool>
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