/tools/picard/picard_BamIndexStats.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 117 lines · 76 code · 33 blank · 8 comment · 0 complexity · de7c4f86d909bdcbed209be39de766a6 MD5 · raw file
- <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>