Mercurial > repos > xuebing > sharplabtool
diff tools/picard/picard_BamIndexStats.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/picard/picard_BamIndexStats.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,117 @@ +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0"> + <requirements><requirement type="package">picard</requirement></requirements> + <command interpreter="python"> + picard_wrapper.py + --input "$input_file" + --bai-file "$input_file.metadata.bam_index" + -t "$htmlfile" + -d "$htmlfile.files_path" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar" + </command> + <inputs> + <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" + help="If empty, upload or import a BAM dataset" /> + </inputs> + <outputs> + <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" /> + </outputs> + <tests> + <test> + <!-- Command + java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt + picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam + --> + <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" /> + <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/> + </test> + <test> + <!-- Command + java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt + picard_BIS_input1.bam can be created from picard_BIS_input1.sam + --> + <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" /> + <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" /> + </test> + </tests> + <help> + +.. class:: infomark + +**Purpose** + +Generate Bam Index Stats for a provided BAM file. + +**Picard documentation** + +This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +------ + +.. class:: infomark + +**Inputs and outputs** + +The only input is the BAM file you wish to obtain statistics for, which is required. +Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files. + +This tool outputs an HTML file that contains links to the actual metrics results, as well +as a log file with info on the exact command run. + +.. class:: warningmark + +**Warning on SAM/BAM quality** + +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** +flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with SAM/BAM that cannot be parsed. + +------ + +**Example** + +Given a BAM file created from the following:: + + @HD VN:1.0 SO:coordinate + @SQ SN:chr1 LN:101 + @SQ SN:chr7 LN:404 + @SQ SN:chr8 LN:202 + @SQ SN:chr10 LN:303 + @SQ SN:chr14 LN:505 + @RG ID:0 SM:Hi,Mom! + @RG ID:1 SM:samplesample DS:ClearDescription + @PG ID:1 PN:Hey! VN:2.0 + @CO Just a generic comment to make the header longer + 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 + 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 + 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 + 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 + 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 + 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 + 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 + 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 + +The following metrics file will be produced:: + + chr1 length= 101 Aligned= 0 Unaligned= 0 + chr7 length= 404 Aligned= 7 Unaligned= 0 + chr8 length= 202 Aligned= 0 Unaligned= 0 + chr10 length= 303 Aligned= 0 Unaligned= 0 + chr14 length= 505 Aligned= 0 Unaligned= 0 + NoCoordinateCount= 1 + + </help> +</tool> + + + + + + + + + + + +