/tools/picard/picard_BamIndexStats.xml

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