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comparison BAM_preprocessingPairs.xml @ 2:89b207100214 draft

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author bzeitouni
date Mon, 11 Jun 2012 12:29:57 -0400
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1 <tool id="svdetect_preprocessing" name="BAM preprocessing">
2
3 <description>to get abnormal pairs</description>
4
5 <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name
6 #if $newBam.pairNormal=="yes"
7 -d -x '$normBAM'
8 #end if
9 '$inputBam'
10 </command>
11
12 <inputs>
13 <param name="sample_name" type="text" value="sample" label="Sample Name"/>
14 <param name="inputBam" type="data" format="bam" label="BAM input file"/>
15 <param name="readType" type="select" label="Read type">
16 <option value="1">Illumina</option>
17 <option value="0">SOLiD</option>
18 </param>
19 <param name="pairType" type="select" label="Library type">
20 <option value="1">Paired-end</option>
21 <option value="0">Mate-Pair</option>
22 </param>
23 <conditional name="newBam">
24 <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam">
25 <option value="no">No</option>
26 <option value="yes">Yes</option>
27 </param>
28 <when value="yes">
29 <!-- do nothing here -->
30 </when>
31 <when value="no">
32 <!-- do nothing here -->
33 </when>
34 </conditional>
35 <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/>
36 <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/>
37 <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/>
38 <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/>
39 </inputs>
40
41 <outputs>
42 <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/>
43 <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/>
44 <data format="bam" name="normBAM" label="${$sample_name}.norm.bam">
45 <filter>newBam['pairNormal'] == 'yes'</filter>
46 </data>
47 </outputs>
48
49 <help>
50
51 **What it does**
52
53 Bam_preprocessingPairs - Version 0.4b
54
55 Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect.
56
57 From all pairs mapped onto the reference genome, this script outputs abnormal pairs:
58
59 * mapped on two different chromosomes
60 * with an incorrect strand orientation and/or pair order
61 * with an insert size distance +- sigma threshold
62
63 into a file prefix.ab.bam/sam sorted by read names
64
65 -BAM/SAM File input format only.
66
67 SAMtools required for BAM files
68
69 -----
70
71 .. class:: infomark
72
73 Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
74
75 </help>
76
77 </tool>