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annotate picard_CollectInsertSizeMetrics.xml @ 11:3d8d70436d02 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:41:25 -0500
parents 41b8d087a2d2
children 486d7500da69
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1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.0">
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2 <description>plots distribution of insert sizes</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.3.1">r</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 @java_options@
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11 @symlink_element_identifier@
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12 ##set up input files
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14 #set $reference_fasta_filename = "localref.fa"
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16 #if str( $reference_source.reference_source_selector ) == "history":
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17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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18 #else:
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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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20 #end if
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22 picard
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23 CollectInsertSizeMetrics
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24 INPUT='$escaped_element_identifier'
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25 OUTPUT="${outFile}"
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26 HISTOGRAM_FILE="${histFile}"
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27 DEVIATIONS="${deviations}"
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29 #if str( $hist_width ):
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30 HISTOGRAM_WIDTH="${hist_width}"
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31 #end if
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33 MINIMUM_PCT="${min_pct}"
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34 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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35 ASSUME_SORTED="${assume_sorted}"
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36 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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38 VALIDATION_STRINGENCY="${validation_stringency}"
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39 QUIET=true
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40 VERBOSITY=ERROR
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41
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42 ]]></command>
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43 <inputs>
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44 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
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45 <conditional name="reference_source">
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46 <param name="reference_source_selector" type="select" label="Load reference genome from">
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47 <option value="cached">Local cache</option>
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48 <option value="history">History</option>
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49 </param>
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50 <when value="cached">
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51 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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52 <options from_data_table="all_fasta">
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53 </options>
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54 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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55 </param>
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56 </when>
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57 <when value="history">
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58 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
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59 </when>
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60 </conditional>
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61 <param name="deviations" type="float" value="10.0" label="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" help="DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0"/>
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62 <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/>
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63 <param name="min_pct" type="float" value="0.05" label="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" help="MINIMUM_PCT; (Range: 0 to 1). default=0.05. "/>
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64 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
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65 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
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66 <option value="ALL_READS" selected="True">All reads</option>
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67 <option value="SAMPLE">Sample</option>
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68 <option value="LIBRARY">Library</option>
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69 <option value="READ_GROUP">Read group</option>
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70 </param>
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71
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72 <expand macro="VS" />
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73
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74 </inputs>
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75
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76 <outputs>
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77 <data format="tabular" name="outFile"/>
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78 <data format="pdf" name="histFile"/>
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79 </outputs>
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80
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81 <tests>
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82 <test>
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83 <param name="metric_accumulation_level" value="ALL_READS"/>
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84 <param name="deviations" value="10.0" />
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85 <param name="hist_width" value="500" />
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86 <param name="min_pct" value="0.05" />
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87 <param name="assume_sorted" value="true" />
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88 <param name="reference_source_selector" value="history" />
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89 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
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90 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
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91 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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92 </test>
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93 </tests>
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94
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95
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96 <help>
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97
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98 .. class:: infomark
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99
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100 **Purpose**
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101
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102 Reads a SAM or BAM dataset and writes a file containing metrics about the statistical distribution of insert size (excluding duplicates) and generates a Histogram plot.
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103
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104 @dataset_collections@
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105
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106 @description@
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107
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108
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109 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
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110 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
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111 includes enough anomalous values from chimeras and other artifacts to make the mean and
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112 sd grossly misleading regarding the real distribution. Default value: 10.0.
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113
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114 HISTOGRAM_WIDTH=Integer
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115 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
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116 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
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117 included. Default value: not set.
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118
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119 MINIMUM_PCT=Float
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120 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
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121 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
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122
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123 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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124 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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125 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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126
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127 ASSUME_SORTED=Boolean
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128 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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129 value: true. This option can be set to 'null' to clear the default value. Possible
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130 values: {true, false}
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131
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132 @more_info@
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133
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134 </help>
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135 </tool>
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136
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137