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comparison picard_BamIndexStats.xml @ 0:ff4ec13e496e draft

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author devteam
date Tue, 23 Oct 2012 10:49:35 -0400
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1 <tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
3 <command interpreter="python">
4 picard_wrapper.py
5 --input "$input_file"
6 --bai-file "$input_file.metadata.bam_index"
7 -t "$htmlfile"
8 -d "$htmlfile.files_path"
9 -j "\$JAVA_JAR_PATH/BamIndexStats.jar"
10 --tmpdir "${__new_file_path__}"
11 </command>
12 <inputs>
13 <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for"
14 help="If empty, upload or import a BAM dataset" />
15 </inputs>
16 <outputs>
17 <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" />
18 </outputs>
19 <tests>
20 <test>
21 <!-- Command
22 java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt
23 picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam
24 -->
25 <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" />
26 <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/>
27 </test>
28 <test>
29 <!-- Command
30 java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt
31 picard_BIS_input1.bam can be created from picard_BIS_input1.sam
32 -->
33 <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" />
34 <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" />
35 </test>
36 </tests>
37 <help>
38
39 .. class:: infomark
40
41 **Purpose**
42
43 Generate Bam Index Stats for a provided BAM file.
44
45 **Picard documentation**
46
47 This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_.
48
49 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
50
51 ------
52
53 .. class:: infomark
54
55 **Inputs and outputs**
56
57 The only input is the BAM file you wish to obtain statistics for, which is required.
58 Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files.
59
60 This tool outputs an HTML file that contains links to the actual metrics results, as well
61 as a log file with info on the exact command run.
62
63 .. class:: warningmark
64
65 **Warning on SAM/BAM quality**
66
67 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
68 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
69 to be the only way to deal with SAM/BAM that cannot be parsed.
70
71 ------
72
73 **Example**
74
75 Given a BAM file created from the following::
76
77 @HD VN:1.0 SO:coordinate
78 @SQ SN:chr1 LN:101
79 @SQ SN:chr7 LN:404
80 @SQ SN:chr8 LN:202
81 @SQ SN:chr10 LN:303
82 @SQ SN:chr14 LN:505
83 @RG ID:0 SM:Hi,Mom!
84 @RG ID:1 SM:samplesample DS:ClearDescription
85 @PG ID:1 PN:Hey! VN:2.0
86 @CO Just a generic comment to make the header longer
87 read1 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0
88 read2 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0
89 read3 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0
90 read4 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0
91 read5 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0
92 read6 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0
93 read7 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0
94 read8 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0
95
96 The following metrics file will be produced::
97
98 chr1 length= 101 Aligned= 0 Unaligned= 0
99 chr7 length= 404 Aligned= 7 Unaligned= 0
100 chr8 length= 202 Aligned= 0 Unaligned= 0
101 chr10 length= 303 Aligned= 0 Unaligned= 0
102 chr14 length= 505 Aligned= 0 Unaligned= 0
103 NoCoordinateCount= 1
104
105 </help>
106 </tool>
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