Mercurial > repos > devteam > picard_122_up
comparison picard_EstimateLibraryComplexity.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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1 <tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="1.122.0"> | |
2 <description>assess sequence library complexity from read sequences</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 <command> | |
12 @java_options@ | |
13 | |
14 java -jar \$JAVA_JAR_PATH/EstimateLibraryComplexity.jar | |
15 | |
16 INPUT="${inputFile}" | |
17 OUTPUT="${outFile}" | |
18 | |
19 MIN_IDENTICAL_BASES="${min_identical_bases}" | |
20 MAX_DIFF_RATE="${max_diff_rate}" | |
21 MIN_MEAN_QUALITY="${min_mean_quality}" | |
22 MAX_GROUP_RATIO="${max_group_ratio}" | |
23 READ_NAME_REGEX="${read_name_regex}" | |
24 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" | |
25 | |
26 VALIDATION_STRINGENCY="${validation_stringency}" | |
27 QUIET=true | |
28 VERBOSITY=ERROR | |
29 | |
30 </command> | |
31 <inputs> | |
32 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
33 <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; 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=5"/> | |
34 <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/> | |
35 <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/> | |
36 <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/> | |
37 | |
38 <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; 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. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> | |
39 <sanitizer> | |
40 <valid initial="string.printable"> | |
41 </valid> | |
42 </sanitizer> | |
43 </param> | |
44 <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> | |
45 | |
46 <expand macro="VS" /> | |
47 | |
48 </inputs> | |
49 | |
50 <outputs> | |
51 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/> | |
52 </outputs> | |
53 | |
54 <tests> | |
55 <test> | |
56 <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/> | |
57 <param name="min_identical_bases" value="5"/> | |
58 <param name="max_diff_rate" value="0.03"/> | |
59 <param name="min_mean_quality" value="20"/> | |
60 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> | |
61 <param name="optical_duplicate_pixel_distance" value="100"/> | |
62 <param name="max_group_ratio" value="500"/> | |
63 <param name="validation_stringency" value="LENIENT"/> | |
64 <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/> | |
65 </test> | |
66 </tests> | |
67 | |
68 <stdio> | |
69 <exit_code range="1:" level="fatal"/> | |
70 </stdio> | |
71 | |
72 <help> | |
73 | |
74 **Purpose** | |
75 | |
76 Attempts to estimate library complexity from sequence of read pairs alone. Does so by sorting all reads by the first N bases (5 by default) | |
77 of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates | |
78 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). | |
79 | |
80 Reads of poor quality are filtered out so as to provide a more accurate estimate. The filtering removes reads with any no-calls in the first | |
81 N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read. | |
82 | |
83 Unpaired reads are ignored in this computation. | |
84 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size. | |
85 | |
86 Also, since there is no alignment to screen out technical reads one further filter is applied on the data. After examining all reads a Histogram | |
87 is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram | |
88 as outliers before library size is estimated. | |
89 | |
90 @dataset_collections@ | |
91 | |
92 @description@ | |
93 | |
94 MIN_IDENTICAL_BASES=Integer The minimum number of bases at the starts of reads that must be identical for reads to be | |
95 grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads | |
96 will be compared at a time, so lower numbers will produce more accurate results but | |
97 consume exponentially more memory and CPU. Default value: 5. | |
98 | |
99 MAX_DIFF_RATE=Double The maximum rate of differences between two reads to call them identical. Default value: | |
100 0.03. | |
101 | |
102 MIN_MEAN_QUALITY=Integer The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads | |
103 with lower average quality are filtered out and not considered in any calculations. | |
104 Default value: 20. | |
105 | |
106 MAX_GROUP_RATIO=Integer Do not process self-similar groups that are this many times over the mean expected group | |
107 size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then | |
108 the mean expected group size would be approximately 10 reads. Default value: 500. | |
109 | |
110 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read | |
111 names are parsed to extract three variables: tile/region, x coordinate and y coordinate. | |
112 These values are used to estimate the rate of optical duplication in order to give a more | |
113 accurate estimated library size. Set this option to null to disable optical duplicate | |
114 detection. The regular expression should contain three capture groups for the three | |
115 variables, in order. It must match the entire read name. Note that if the default regex | |
116 is specified, a regex match is not actually done, but instead the read name is split on | |
117 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be | |
118 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements | |
119 are assumed to be tile, x and y values. Default value: | |
120 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. | |
121 | |
122 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer | |
123 The maximum offset between two duplicte clusters in order to consider them optical | |
124 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) | |
125 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in | |
126 which case 50-100 is more normal. Default value: 100. | |
127 | |
128 | |
129 @more_info@ | |
130 | |
131 </help> | |
132 </tool> | |
133 | |
134 |