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1 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
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2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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3 <command interpreter="python">
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4 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}"
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5 --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
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6 -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}"
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7 </command>
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8 <inputs>
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9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
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10 help="If empty, upload or import a SAM/BAM dataset."/>
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11 <param name="out_prefix" value="Library Complexity" type="text"
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12 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
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13 <param name="minIDbases" value="5" type="integer" label="Minimum identical bases at starts of reads for grouping" size="5"
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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." />
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15 <param name="maxDiff" value="0.03" type="float"
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16 label="Maximum difference rate for identical reads" size="5"
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17 help="The maximum rate of differences between two reads to call them identical" />
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18 <param name="minMeanQ" value="20" type="integer"
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19 label="Minimum percentage" size="5"
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20 help="The minimum mean quality of bases in a read pair. Lower average quality reads filtered out from all calculations" />
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21 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="120"
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22 label="Regular expression that can be used to parse read names in the incoming SAM file"
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23 help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" >
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24 <sanitizer>
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25 <valid initial="string.printable">
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26 <remove value="'"/>
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27 </valid>
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28 <mapping initial="none">
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29 <add source="'" target="__sq__"/>
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30 </mapping>
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31 </sanitizer>
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32 </param>
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33 <param name="optDupeDist" value="100" type="text"
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34 label="The maximum offset between two duplicte clusters in order to consider them optical duplicates." size="5"
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35 help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100" />
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36
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37 </inputs>
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38 <outputs>
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39 <data format="html" name="html_file" label="${out_prefix}_lib_complexity.html"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input_file" value="picard_input_tiny.sam" />
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44 <param name="out_prefix" value="Library Complexity" />
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45 <param name="minIDbases" value="5" />
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46 <param name="maxDiff" value="0.03" />
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47 <param name="minMeanQ" value="20" />
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48 <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" />
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49 <param name="optDupeDist" value="100" />
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50 <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="30" />
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51 </test>
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52 </tests>
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53 <help>
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54
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55 .. class:: infomark
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56
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57 **Purpose**
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58
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59 Attempts to estimate library complexity from sequence alone.
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60 Does so by sorting all reads by the first N bases (5 by default) of each read and then
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61 comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be
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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).
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63
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64 Reads of poor quality are filtered out so as to provide a more accurate estimate.
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65 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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66 MIN_MEAN_QUALITY across either the first or second read.
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67
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68 The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the
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69 calculation of library size. Also, since there is no alignment to screen out technical reads one
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70 further filter is applied on the data. After examining all reads a histogram is built of
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71 [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are
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72 then removed from the histogram as outliers before library size is estimated.
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73
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74 **Picard documentation**
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75
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76 This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_.
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77
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78 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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79
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80 -----
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81
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82 .. class:: infomark
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83
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84 **Inputs, outputs, and parameters**
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85
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86 Picard documentation says (reformatted for Galaxy):
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87
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88 .. csv-table::
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89 :header-rows: 1
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90
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91 Option Description
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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."
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93 "OUTPUT=File","Output file to writes per-library metrics to. Required."
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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."
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95 "MAX_DIFF_RATE=Double","The maximum rate of differences between two reads to call them identical. Default value: 0.03. "
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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."
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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."
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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"
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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. "
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100
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101 .. class:: warningmark
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102
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103 **Warning on SAM/BAM quality**
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104
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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**
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106 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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107 to be the only way to deal with SAM/BAM that cannot be parsed.
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108
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109 .. class:: infomark
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110
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111 **Note on the Regular Expression**
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112
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113 (from the Picard docs)
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114 This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file.
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115 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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116 The regular expression should contain three capture groups for the three variables, in order.
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117 Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.
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118
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119
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120 </help>
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121 </tool>
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122
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123
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