Mercurial > repos > devteam > picard
annotate picard_EstimateLibraryComplexity.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 4ff1e04010e6 |
| children | 5eaa8a968300 |
| rev | line source |
|---|---|
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8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
6
diff
changeset
|
1 <tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>assess sequence library complexity from read sequences</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </macros> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
6
diff
changeset
|
6 <expand macro="requirements" /> |
| 5 | 7 <command> |
| 8 @java_options@ | |
| 9 | |
| 10 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 11 EstimateLibraryComplexity | |
| 12 | |
| 13 INPUT="${inputFile}" | |
| 14 OUTPUT="${outFile}" | |
| 15 | |
| 16 MIN_IDENTICAL_BASES="${min_identical_bases}" | |
| 17 MAX_DIFF_RATE="${max_diff_rate}" | |
| 18 MIN_MEAN_QUALITY="${min_mean_quality}" | |
| 19 MAX_GROUP_RATIO="${max_group_ratio}" | |
| 6 | 20 #import pipes |
| 21 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } | |
| 5 | 22 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" |
| 23 | |
| 24 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 25 QUIET=true | |
| 26 VERBOSITY=ERROR | |
| 27 | |
| 28 </command> | |
| 29 <inputs> | |
| 30 <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" /> | |
| 31 <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"/> | |
| 32 <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"/> | |
| 33 <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"/> | |
| 34 <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"/> | |
| 35 | |
| 36 <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]+).*."> | |
| 37 <sanitizer> | |
| 38 <valid initial="string.printable"> | |
| 39 </valid> | |
| 40 </sanitizer> | |
| 41 </param> | |
| 42 <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"/> | |
| 43 | |
| 44 <expand macro="VS" /> | |
| 45 | |
| 46 </inputs> | |
| 47 | |
| 48 <outputs> | |
| 49 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/> | |
| 50 </outputs> | |
| 51 | |
| 52 <tests> | |
| 53 <test> | |
| 54 <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/> | |
| 55 <param name="min_identical_bases" value="5"/> | |
| 56 <param name="max_diff_rate" value="0.03"/> | |
| 57 <param name="min_mean_quality" value="20"/> | |
| 58 <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> | |
| 59 <param name="optical_duplicate_pixel_distance" value="100"/> | |
| 60 <param name="max_group_ratio" value="500"/> | |
| 61 <param name="validation_stringency" value="LENIENT"/> | |
| 62 <output name="outFile" file="picard_EstimateLibraryComplexity_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 63 </test> | |
| 64 </tests> | |
| 65 | |
| 66 <stdio> | |
| 67 <exit_code range="1:" level="fatal"/> | |
| 68 </stdio> | |
| 69 | |
| 70 <help> | |
| 71 | |
| 72 **Purpose** | |
| 73 | |
| 74 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) | |
| 75 of each read and then comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be duplicates | |
| 76 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). | |
| 77 | |
| 78 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 | |
| 79 N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read. | |
| 80 | |
| 81 Unpaired reads are ignored in this computation. | |
| 82 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size. | |
| 83 | |
| 84 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 | |
| 85 is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram | |
| 86 as outliers before library size is estimated. | |
| 87 | |
| 88 @dataset_collections@ | |
| 89 | |
| 90 @description@ | |
| 91 | |
| 92 MIN_IDENTICAL_BASES=Integer The minimum number of bases at the starts of reads that must be identical for reads to be | |
| 93 grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads | |
| 94 will be compared at a time, so lower numbers will produce more accurate results but | |
| 95 consume exponentially more memory and CPU. Default value: 5. | |
| 96 | |
| 97 MAX_DIFF_RATE=Double The maximum rate of differences between two reads to call them identical. Default value: | |
| 98 0.03. | |
| 99 | |
| 100 MIN_MEAN_QUALITY=Integer The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads | |
| 101 with lower average quality are filtered out and not considered in any calculations. | |
| 102 Default value: 20. | |
| 103 | |
| 104 MAX_GROUP_RATIO=Integer Do not process self-similar groups that are this many times over the mean expected group | |
| 105 size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then | |
| 106 the mean expected group size would be approximately 10 reads. Default value: 500. | |
| 107 | |
| 108 READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read | |
| 109 names are parsed to extract three variables: tile/region, x coordinate and y coordinate. | |
| 110 These values are used to estimate the rate of optical duplication in order to give a more | |
| 111 accurate estimated library size. Set this option to null to disable optical duplicate | |
| 112 detection. The regular expression should contain three capture groups for the three | |
| 113 variables, in order. It must match the entire read name. Note that if the default regex | |
| 114 is specified, a regex match is not actually done, but instead the read name is split on | |
| 115 colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be | |
| 116 tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements | |
| 117 are assumed to be tile, x and y values. Default value: | |
| 118 [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. | |
| 119 | |
| 120 OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer | |
| 121 The maximum offset between two duplicte clusters in order to consider them optical | |
| 122 duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) | |
| 123 unless using later versions of the Illumina pipeline that multiply pixel values by 10, in | |
| 124 which case 50-100 is more normal. Default value: 100. | |
| 125 | |
| 126 | |
| 127 @more_info@ | |
| 128 | |
| 129 </help> | |
| 130 </tool> | |
| 131 | |
| 132 |