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comparison svdetect/SVDetect_import.xml @ 20:42353a10899a draft

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author bzeitouni
date Thu, 12 Jul 2012 12:10:27 -0400
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1 <tool id="svdetect_import" name="Import data">
2 <description>BAM, chromosome info or sv files</description>
3 <command interpreter="bash">SVDetect_import.sh -i $file_path
4 #if str($type.file_type)=="bam"
5 -o $outbamfile
6 #elif str($type.file_type)=="len"
7 -o $outlenfile
8 #elif str($type.file_type)=="sv"
9 -o $outsvfile
10 #end if
11 </command>
12 <inputs>
13 <param name="file_name" type="text" value="file1" label="File Name"/>
14 <conditional name="type">
15 <param name="file_type" type="select" label="Select the file type to import" help="BAM file (BAM) or text file (SAM, chromosome list or a SV tabulated text file)">
16 <option value="bam">BAM file (.bam)</option>
17 <option value="len">Chromosome info file (.len)</option>
18 <option value="sv">SVDetect output file (.sv)</option>
19 </param>
20 <when value="bam">
21 <!-- do nothing here -->
22 </when>
23 <when value="len">
24 <!-- do nothing here -->
25 </when>
26 <when value="sv">
27 <!-- do nothing here -->
28 </when>
29 </conditional>
30 <param name="file_path" type="text" size="150" label="Path to file"/>
31 </inputs>
32 <outputs>
33 <data format="bam" name="outbamfile" label="${file_name}.bam">
34 <filter>type['file_type']=="bam"</filter>
35 </data>
36 <data format="len" name="outlenfile" label="${file_name}.len">
37 <filter>type['file_type']=="len"</filter>
38 </data>
39 <data format="sv" name="outsvfile" label="${file_name}.sv">
40 <filter>type['file_type']=="sv"</filter>
41 </data>
42 </outputs>
43 <help>
44 **What it does**
45
46 This tool allows you to import quickly a BAM file, a chromosome info file or a SVDetect output file from you computer as inputs for SVDetect.
47
48
49 **Example of chromosome file**
50
51 Input len file::
52
53 1 chr1 247249719
54 2 chr2 242951149
55 3 chr3 199501827
56 4 chr4 191273063
57 5 chr5 180857866
58 6 chr6 170899992
59 7 chr7 158821424
60 8 chr8 146274826
61 9 chr9 140273252
62 10 chr10 135374737
63 11 chr11 134452384
64 12 chr12 132349534
65 13 chr13 114142980
66 14 chr14 106368585
67 15 chr15 100338915
68 16 chr16 88827254
69 17 chr17 78774742
70 18 chr18 76117153
71 19 chr19 63811651
72 20 chr20 62435964
73 21 chr21 46944323
74 22 chr22 49691432
75 23 chrX 154913754
76 24 chrY 57772954
77
78 -----
79
80 .. class:: infomark
81
82 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
83 </help>
84
85 </tool>