Mercurial > repos > devteam > picard
annotate rgPicardHsMetrics.xml @ 4:ab1f60c26526 draft
Uploaded valid tools and complex repository dependency definition.
| author | devteam |
|---|---|
| date | Fri, 21 Feb 2014 12:07:49 -0500 |
| parents | 9227b8c3093b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0"> |
| 2 <description>for targeted resequencing data</description> | |
| 3 <command interpreter="python"> | |
| 4 | |
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2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
6 --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" |
| 0 | 7 -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar" |
| 8 | |
| 9 </command> | |
| 10 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 11 <inputs> | |
| 12 <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" /> | |
| 13 <param name="out_prefix" value="Picard HS Metrics" type="text" label="Title for the output file" help="Use to remind you what the job was for." size="80" /> | |
| 14 <param name="bait_bed" type="data" format="bed,interval" label="Bait intervals: Sequences for bait in the design" help="Note specific format requirements below!" size="80" /> | |
| 15 <param name="target_bed" type="data" format="bed,interval" label="Target intervals: Sequences for targets in the design" help="Note specific format requirements below!" size="80" /> | |
| 16 <!-- | |
| 17 | |
| 18 Users can be enabled to set Java heap size by uncommenting this option and adding '-x "$maxheap"' to the <command> tag. | |
| 19 If commented out the heapsize defaults to the value specified within picard_wrapper.py | |
| 20 | |
| 21 <param name="maxheap" type="select" | |
| 22 help="If in doubt, try the default. If it fails with a complaint about java heap size, try increasing it please - larger jobs will require your own hardware." | |
| 23 label="Java heap size"> | |
| 24 <option value="4G" selected = "true">4GB default </option> | |
| 25 <option value="8G" >8GB use if 4GB fails</option> | |
| 26 <option value="16G">16GB - try this if 8GB fails</option> | |
| 27 </param> | |
| 28 | |
| 29 --> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data format="html" name="html_file" label="${out_prefix}.html" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <!-- Uncomment this if maxheap parameter is enabled | |
| 37 <param name="maxheap" value="8G" /> | |
| 38 --> | |
| 39 <param name="out_prefix" value="HSMetrics" /> | |
| 40 <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" /> | |
| 41 <param name="bait_bed" value="picard_input_bait.bed" /> | |
| 42 <param name="target_bed" value="picard_input_bait.bed" /> | |
| 43 <output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 | |
| 48 .. class:: infomark | |
| 49 | |
| 50 **Summary** | |
| 51 | |
| 52 Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file. | |
| 53 | |
| 54 .. class:: warnmark | |
| 55 | |
| 56 **WARNING about bait and target files** | |
| 57 | |
| 58 Picard is very fussy about the bait and target file format. If these are not exactly right, it will fail with an error something like: | |
| 59 | |
| 60 Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 6 fields: chr1 45787123 45787316 CASO_22G_25063 1000 + | |
| 61 | |
| 62 If you see an error like that from this tool, please do NOT report it to any of the Galaxy mailing lists as it is not a bug! | |
| 63 It means you must reformat your bait and target files. Galaxy cannot do that for you automatically unfortunately. | |
| 64 | |
| 65 The required definition is described in the documentation at http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_command-line_arguments | |
| 66 and the sample provided looks like this: | |
| 67 | |
| 68 chr1 1104841 1104940 + target_1 | |
| 69 chr1 1105283 1105599 + target_2 | |
| 70 chr1 1105712 1105860 + target_3 | |
| 71 chr1 1105960 1106119 + target_4 | |
| 72 | |
| 73 So your bait and target files MUST have 5 columns with chr, start, end, strand and name tab delimited and in exactly that order. | |
| 74 Note that the Picard mandated sam header described in the documentation linked above is automagically added by the tool in Galaxy. | |
| 75 | |
| 76 .. class:: infomark | |
| 77 | |
| 78 **Picard documentation** | |
| 79 | |
| 80 This is a Galaxy wrapper for CalculateHsMetrics.jar, a part of the external package Picard-tools_. | |
| 81 | |
| 82 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 83 | |
| 84 ----- | |
| 85 | |
| 86 .. class:: infomark | |
| 87 | |
| 88 **Inputs, outputs, and parameters** | |
| 89 | |
| 90 Picard documentation says (reformatted for Galaxy): | |
| 91 | |
| 92 Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file. | |
| 93 | |
| 94 .. csv-table:: | |
| 95 :header-rows: 1 | |
| 96 | |
| 97 "Option", "Description" | |
| 98 "BAIT_INTERVALS=File","An interval list file that contains the locations of the baits used. Required." | |
| 99 "TARGET_INTERVALS=File","An interval list file that contains the locations of the targets. Required." | |
| 100 "INPUT=File","An aligned SAM or BAM file. Required." | |
| 101 "OUTPUT=File","The output file to write the metrics to. Required. Cannot be used in conjuction with option(s) METRICS_FILE (M)" | |
| 102 "METRICS_FILE=File","Legacy synonym for OUTPUT, should not be used. Required. Cannot be used in conjuction with option(s) OUTPUT (O)" | |
| 103 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" | |
| 104 | |
| 105 HsMetrics | |
| 106 | |
| 107 The set of metrics captured that are specific to a hybrid selection analysis. | |
| 108 | |
| 109 Output Column Definitions:: | |
| 110 | |
| 111 1. BAIT_SET: The name of the bait set used in the hybrid selection. | |
| 112 2. GENOME_SIZE: The number of bases in the reference genome used for alignment. | |
| 113 3. BAIT_TERRITORY: The number of bases which have one or more baits on top of them. | |
| 114 4. TARGET_TERRITORY: The unique number of target bases in the experiment where target is usually exons etc. | |
| 115 5. BAIT_DESIGN_EFFICIENCY: Target terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target. | |
| 116 6. TOTAL_READS: The total number of reads in the SAM or BAM file examine. | |
| 117 7. PF_READS: The number of reads that pass the vendor's filter. | |
| 118 8. PF_UNIQUE_READS: The number of PF reads that are not marked as duplicates. | |
| 119 9. PCT_PF_READS: PF reads / total reads. The percent of reads passing filter. | |
| 120 10. PCT_PF_UQ_READS: PF Unique Reads / Total Reads. | |
| 121 11. PF_UQ_READS_ALIGNED: The number of PF unique reads that are aligned with mapping score > 0 to the reference genome. | |
| 122 12. PCT_PF_UQ_READS_ALIGNED: PF Reads Aligned / PF Reads. | |
| 123 13. PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps. | |
| 124 14. ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited region of the genome. | |
| 125 15. NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region. | |
| 126 16. OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on or near a bait. | |
| 127 17. ON_TARGET_BASES: The number of PF aligned bases that mapped to a targetted region of the genome. | |
| 128 18. PCT_SELECTED_BASES: On+Near Bait Bases / PF Bases Aligned. | |
| 129 19. PCT_OFF_BAIT: The percentage of aligned PF bases that mapped neither on or near a bait. | |
| 130 20. ON_BAIT_VS_SELECTED: The percentage of on+near bait bases that are on as opposed to near. | |
| 131 21. MEAN_BAIT_COVERAGE: The mean coverage of all baits in the experiment. | |
| 132 22. MEAN_TARGET_COVERAGE: The mean coverage of targets that recieved at least coverage depth = 2 at one base. | |
| 133 23. PCT_USABLE_BASES_ON_BAIT: The number of aligned, de-duped, on-bait bases out of the PF bases available. | |
| 134 24. PCT_USABLE_BASES_ON_TARGET: The number of aligned, de-duped, on-target bases out of the PF bases available. | |
| 135 25. FOLD_ENRICHMENT: The fold by which the baited region has been amplified above genomic background. | |
| 136 26. ZERO_CVG_TARGETS_PCT: The number of targets that did not reach coverage=2 over any base. | |
| 137 27. FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets. | |
| 138 28. PCT_TARGET_BASES_2X: The percentage of ALL target bases acheiving 2X or greater coverage. | |
| 139 29. PCT_TARGET_BASES_10X: The percentage of ALL target bases acheiving 10X or greater coverage. | |
| 140 30. PCT_TARGET_BASES_20X: The percentage of ALL target bases acheiving 20X or greater coverage. | |
| 141 31. PCT_TARGET_BASES_30X: The percentage of ALL target bases acheiving 30X or greater coverage. | |
| 142 32. HS_LIBRARY_SIZE: The estimated number of unique molecules in the selected part of the library. | |
| 143 33. HS_PENALTY_10X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 10 * HS_PENALTY_10X. | |
| 144 34. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X. | |
| 145 35. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X. | |
| 146 | |
| 147 .. class:: warningmark | |
| 148 | |
| 149 **Warning on SAM/BAM quality** | |
| 150 | |
| 151 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** | |
| 152 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. | |
| 153 | |
| 154 | |
| 155 </help> | |
| 156 </tool> |