|
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">
|
|
|
4 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
|
|
|
5 --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
|
|
|
6 -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
|
|
|
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
|
