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1 <tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
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2 <requirements><requirement type="package" version="1.56.0">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 "\$JAVA_JAR_PATH/BamIndexStats.jar"
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10 --tmpdir "${__new_file_path__}"
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11 </command>
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12 <inputs>
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13 <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for"
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14 help="If empty, upload or import a BAM dataset" />
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15 </inputs>
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16 <outputs>
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17 <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <!-- Command
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22 java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt
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23 picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam
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24 -->
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25 <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" />
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26 <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/>
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27 </test>
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28 <test>
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29 <!-- Command
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30 java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt
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31 picard_BIS_input1.bam can be created from picard_BIS_input1.sam
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32 -->
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33 <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" />
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34 <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" />
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35 </test>
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36 </tests>
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **Purpose**
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42
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43 Generate Bam Index Stats for a provided BAM file.
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44
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45 **Picard documentation**
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46
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47 This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_.
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48
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49 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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50
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51 ------
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52
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53 .. class:: infomark
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54
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55 **Inputs and outputs**
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56
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57 The only input is the BAM file you wish to obtain statistics for, which is required.
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58 Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files.
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59
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60 This tool outputs an HTML file that contains links to the actual metrics results, as well
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61 as a log file with info on the exact command run.
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62
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63 .. class:: warningmark
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64
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65 **Warning on SAM/BAM quality**
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66
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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**
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68 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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69 to be the only way to deal with SAM/BAM that cannot be parsed.
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70
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71 ------
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72
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73 **Example**
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74
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75 Given a BAM file created from the following::
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76
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77 @HD VN:1.0 SO:coordinate
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78 @SQ SN:chr1 LN:101
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79 @SQ SN:chr7 LN:404
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80 @SQ SN:chr8 LN:202
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81 @SQ SN:chr10 LN:303
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82 @SQ SN:chr14 LN:505
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83 @RG ID:0 SM:Hi,Mom!
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84 @RG ID:1 SM:samplesample DS:ClearDescription
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85 @PG ID:1 PN:Hey! VN:2.0
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86 @CO Just a generic comment to make the header longer
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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
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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
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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
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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
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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
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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
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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
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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
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95
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96 The following metrics file will be produced::
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97
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98 chr1 length= 101 Aligned= 0 Unaligned= 0
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99 chr7 length= 404 Aligned= 7 Unaligned= 0
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100 chr8 length= 202 Aligned= 0 Unaligned= 0
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101 chr10 length= 303 Aligned= 0 Unaligned= 0
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102 chr14 length= 505 Aligned= 0 Unaligned= 0
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103 NoCoordinateCount= 1
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104
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105 </help>
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106 </tool>
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107
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