annotate tools/picard/picard_BamIndexStats.xml @ 2:c2a356708570

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author xuebing
date Fri, 09 Mar 2012 19:45:42 -0500
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1 <tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0">
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2 <requirements><requirement type="package">picard</requirement></requirements>
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3 <command interpreter="python">
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4 picard_wrapper.py
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5 --input "$input_file"
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6 --bai-file "$input_file.metadata.bam_index"
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7 -t "$htmlfile"
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8 -d "$htmlfile.files_path"
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9 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar"
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10 </command>
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11 <inputs>
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12 <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for"
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13 help="If empty, upload or import a BAM dataset" />
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14 </inputs>
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15 <outputs>
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16 <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <!-- Command
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21 java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt
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22 picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam
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23 -->
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24 <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" />
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25 <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/>
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26 </test>
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27 <test>
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28 <!-- Command
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29 java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt
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30 picard_BIS_input1.bam can be created from picard_BIS_input1.sam
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31 -->
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32 <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" />
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33 <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" />
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34 </test>
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35 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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40 **Purpose**
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41
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42 Generate Bam Index Stats for a provided BAM file.
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43
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44 **Picard documentation**
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45
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46 This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_.
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47
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48 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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49
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50 ------
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51
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52 .. class:: infomark
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53
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54 **Inputs and outputs**
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55
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56 The only input is the BAM file you wish to obtain statistics for, which is required.
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57 Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files.
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58
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59 This tool outputs an HTML file that contains links to the actual metrics results, as well
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60 as a log file with info on the exact command run.
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61
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62 .. class:: warningmark
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63
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64 **Warning on SAM/BAM quality**
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65
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66 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**
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67 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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68 to be the only way to deal with SAM/BAM that cannot be parsed.
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69
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70 ------
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71
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72 **Example**
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73
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74 Given a BAM file created from the following::
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75
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76 @HD VN:1.0 SO:coordinate
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77 @SQ SN:chr1 LN:101
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78 @SQ SN:chr7 LN:404
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79 @SQ SN:chr8 LN:202
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80 @SQ SN:chr10 LN:303
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81 @SQ SN:chr14 LN:505
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82 @RG ID:0 SM:Hi,Mom!
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83 @RG ID:1 SM:samplesample DS:ClearDescription
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84 @PG ID:1 PN:Hey! VN:2.0
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85 @CO Just a generic comment to make the header longer
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86 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
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87 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
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88 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
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89 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
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90 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
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91 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
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92 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
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93 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
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94
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95 The following metrics file will be produced::
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96
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97 chr1 length= 101 Aligned= 0 Unaligned= 0
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98 chr7 length= 404 Aligned= 7 Unaligned= 0
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99 chr8 length= 202 Aligned= 0 Unaligned= 0
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100 chr10 length= 303 Aligned= 0 Unaligned= 0
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101 chr14 length= 505 Aligned= 0 Unaligned= 0
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102 NoCoordinateCount= 1
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103
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104 </help>
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105 </tool>
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106
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107
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