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1 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01">
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2 <command interpreter="python">
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3 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
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4 --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
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5 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
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6 </command>
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7 <inputs>
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8 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
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9 help="If empty, upload or import a SAM/BAM dataset."/>
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10 <param name="out_prefix" value="Library Complexity" type="text"
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11 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
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12 <param name="minIDbases" value="5" type="integer" label="Minimum identical bases at starts of reads for grouping" size="5"
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13 help="Total_reads / 4^max_id_bases reads will be compared at a time. Lower numbers = more accurate results and exponentially more time/memory." />
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14 <param name="maxDiff" value="0.03" type="float"
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15 label="Maximum difference rate for identical reads" size="5"
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16 help="The maximum rate of differences between two reads to call them identical" />
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17 <param name="minMeanQ" value="20" type="integer"
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18 label="Minimum percentage" size="5"
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19 help="The minimum mean quality of bases in a read pair. Lower average quality reads filtered out from all calculations" />
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20 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="120"
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21 label="Regular expression that can be used to parse read names in the incoming SAM file"
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22 help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" >
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23 <sanitizer>
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24 <valid initial="string.printable">
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25 <remove value="'"/>
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26 </valid>
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27 <mapping initial="none">
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28 <add source="'" target="__sq__"/>
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29 </mapping>
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30 </sanitizer>
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31 </param>
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32 <param name="optDupeDist" value="100" type="text"
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33 label="The maximum offset between two duplicte clusters in order to consider them optical duplicates." size="5"
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34 help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100" />
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35
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36 </inputs>
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37 <outputs>
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38 <data format="html" name="html_file" label="${out_prefix}_lib_complexity.html"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_file" value="picard_input_tiny.sam" />
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43 <param name="out_prefix" value="Library Complexity" />
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44 <param name="minIDbases" value="5" />
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45 <param name="maxDiff" value="0.03" />
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46 <param name="minMeanQ" value="20" />
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47 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" />
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48 <param name="optDupeDist" value="100" />
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49 <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="30" />
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50 </test>
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51 </tests>
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52 <help>
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53
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54 .. class:: infomark
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55
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56 **Purpose**
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57
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58 Attempts to estimate library complexity from sequence alone.
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59 Does so by sorting all reads by the first N bases (5 by default) of each read and then
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60 comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be
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61 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).
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62
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63 Reads of poor quality are filtered out so as to provide a more accurate estimate.
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64 The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than
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65 MIN_MEAN_QUALITY across either the first or second read.
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66
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67 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the
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68 calculation of library size. Also, since there is no alignment to screen out technical reads one
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69 further filter is applied on the data. After examining all reads a histogram is built of
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70 [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are
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71 then removed from the histogram as outliers before library size is estimated.
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72
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73 **Picard documentation**
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74
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75 This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_.
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76
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77 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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78
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79 -----
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80
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81 .. class:: infomark
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82
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83 **Inputs, outputs, and parameters**
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84
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85 Picard documentation says (reformatted for Galaxy):
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86
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87 .. csv-table::
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88 :header-rows: 1
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89
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90 Option Description
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91 "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."
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92 "OUTPUT=File","Output file to writes per-library metrics to. Required."
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93 "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."
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94 "MAX_DIFF_RATE=Double","The maximum rate of differences between two reads to call them identical. Default value: 0.03. "
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95 "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."
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96 "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."
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97 "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"
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98 "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. "
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99
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100 .. class:: warningmark
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101
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102 **Warning on SAM/BAM quality**
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103
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104 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**
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105 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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106 to be the only way to deal with SAM/BAM that cannot be parsed.
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107
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108 .. class:: infomark
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109
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110 **Note on the Regular Expression**
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111
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112 (from the Picard docs)
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113 This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file.
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114 These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size.
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115 The regular expression should contain three capture groups for the three variables, in order.
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116 Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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117
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118
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119 </help>
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120 </tool>
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121
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122
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