Mercurial > repos > devteam > picard
annotate picard_BamIndexStats.xml @ 3:bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 03 May 2013 17:13:01 -0400 |
| parents | 9227b8c3093b |
| children |
| rev | line source |
|---|---|
| 0 | 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 | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
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5 --input "${input_file}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
6 --bai-file "${input_file.metadata.bam_index}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
7 -t "${htmlfile}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
8 -d "${htmlfile.files_path}" |
| 0 | 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> | |
| 107 | |
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