Mercurial > repos > devteam > picard
annotate rgPicardLibComplexity.xml @ 2:9227b8c3093b
Updated command line format per dev team standards.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Tue, 02 Apr 2013 09:42:36 -0400 |
| parents | 1cd7f3b42609 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0"> |
| 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 3 <command interpreter="python"> | |
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9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
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4 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}" |
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9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" |
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9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
6 -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}" |
| 0 | 7 </command> |
| 8 <inputs> | |
| 9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" | |
| 10 help="If empty, upload or import a SAM/BAM dataset."/> | |
| 11 <param name="out_prefix" value="Library Complexity" type="text" | |
| 12 label="Title for the output file" help="Use this remind you what the job was for." size="80" /> | |
| 13 <param name="minIDbases" value="5" type="integer" label="Minimum identical bases at starts of reads for grouping" size="5" | |
| 14 help="Total_reads / 4^max_id_bases reads will be compared at a time. Lower numbers = more accurate results and exponentially more time/memory." /> | |
| 15 <param name="maxDiff" value="0.03" type="float" | |
| 16 label="Maximum difference rate for identical reads" size="5" | |
| 17 help="The maximum rate of differences between two reads to call them identical" /> | |
| 18 <param name="minMeanQ" value="20" type="integer" | |
| 19 label="Minimum percentage" size="5" | |
| 20 help="The minimum mean quality of bases in a read pair. Lower average quality reads filtered out from all calculations" /> | |
| 21 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="120" | |
| 22 label="Regular expression that can be used to parse read names in the incoming SAM file" | |
| 23 help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" > | |
| 24 <sanitizer> | |
| 25 <valid initial="string.printable"> | |
| 26 <remove value="'"/> | |
| 27 </valid> | |
| 28 <mapping initial="none"> | |
| 29 <add source="'" target="__sq__"/> | |
| 30 </mapping> | |
| 31 </sanitizer> | |
| 32 </param> | |
| 33 <param name="optDupeDist" value="100" type="text" | |
| 34 label="The maximum offset between two duplicte clusters in order to consider them optical duplicates." size="5" | |
| 35 help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100" /> | |
| 36 | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="html" name="html_file" label="${out_prefix}_lib_complexity.html"/> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="input_file" value="picard_input_tiny.sam" /> | |
| 44 <param name="out_prefix" value="Library Complexity" /> | |
| 45 <param name="minIDbases" value="5" /> | |
| 46 <param name="maxDiff" value="0.03" /> | |
| 47 <param name="minMeanQ" value="20" /> | |
| 48 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> | |
| 49 <param name="optDupeDist" value="100" /> | |
| 50 <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="30" /> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 | |
| 55 .. class:: infomark | |
| 56 | |
| 57 **Purpose** | |
| 58 | |
| 59 Attempts to estimate library complexity from sequence alone. | |
| 60 Does so by sorting all reads by the first N bases (5 by default) of each read and then | |
| 61 comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be | |
| 62 duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default). | |
| 63 | |
| 64 Reads of poor quality are filtered out so as to provide a more accurate estimate. | |
| 65 The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than | |
| 66 MIN_MEAN_QUALITY across either the first or second read. | |
| 67 | |
| 68 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the | |
| 69 calculation of library size. Also, since there is no alignment to screen out technical reads one | |
| 70 further filter is applied on the data. After examining all reads a histogram is built of | |
| 71 [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are | |
| 72 then removed from the histogram as outliers before library size is estimated. | |
| 73 | |
| 74 **Picard documentation** | |
| 75 | |
| 76 This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_. | |
| 77 | |
| 78 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 79 | |
| 80 ----- | |
| 81 | |
| 82 .. class:: infomark | |
| 83 | |
| 84 **Inputs, outputs, and parameters** | |
| 85 | |
| 86 Picard documentation says (reformatted for Galaxy): | |
| 87 | |
| 88 .. csv-table:: | |
| 89 :header-rows: 1 | |
| 90 | |
| 91 Option Description | |
| 92 "INPUT=File","One or more files to combine and estimate library complexity from. Reads can be mapped or unmapped. This option may be specified 0 or more times." | |
| 93 "OUTPUT=File","Output file to writes per-library metrics to. Required." | |
| 94 "MIN_IDENTICAL_BASES=Integer","The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU. Default value: 5." | |
| 95 "MAX_DIFF_RATE=Double","The maximum rate of differences between two reads to call them identical. Default value: 0.03. " | |
| 96 "MIN_MEAN_QUALITY=Integer","The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads with lower average quality are filtered out and not considered in any calculations. Default value: 20." | |
| 97 "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. The regular expression should contain three capture groups for the three variables, in order. Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. This option can be set to 'null' to clear the default value." | |
| 98 "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" | |
| 99 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. " | |
| 100 | |
| 101 .. class:: warningmark | |
| 102 | |
| 103 **Warning on SAM/BAM quality** | |
| 104 | |
| 105 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** | |
| 106 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears | |
| 107 to be the only way to deal with SAM/BAM that cannot be parsed. | |
| 108 | |
| 109 .. class:: infomark | |
| 110 | |
| 111 **Note on the Regular Expression** | |
| 112 | |
| 113 (from the Picard docs) | |
| 114 This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. | |
| 115 These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. | |
| 116 The regular expression should contain three capture groups for the three variables, in order. | |
| 117 Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. | |
| 118 | |
| 119 | |
| 120 </help> | |
| 121 </tool> | |
| 122 | |
| 123 |