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annotate picard_CollectInsertSizeMetrics.xml @ 29:1aac2a13842a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:06:40 +0000
parents 2a17c789e0a5
children 585027e65f3b
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1 <tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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 <token name="@WRAPPER_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.4.1">r-base</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @java_options@
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12 @symlink_element_identifier@
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13 ##set up input files
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14
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15 #set $reference_fasta_filename = "localref.fa"
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17 @handle_reference_source@
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19 picard
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20 CollectInsertSizeMetrics
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21 INPUT='$escaped_element_identifier'
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22 OUTPUT="${outFile}"
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23 HISTOGRAM_FILE="${histFile}"
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24 DEVIATIONS="${deviations}"
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25
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26 #if str( $hist_width ):
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27 HISTOGRAM_WIDTH="${hist_width}"
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28 #end if
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29
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30 MINIMUM_PCT="${min_pct}"
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31 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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32 ASSUME_SORTED="${assume_sorted}"
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33 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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34
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35 VALIDATION_STRINGENCY="${validation_stringency}"
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36 QUIET=true
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37 VERBOSITY=ERROR
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38 @TMPDIR_OPTION@
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39
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40 ]]></command>
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41 <inputs>
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42 <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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43 <conditional name="reference_source">
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44 <param name="reference_source_selector" type="select" label="Load reference genome from">
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45 <option value="cached">Local cache</option>
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46 <option value="history">History</option>
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47 </param>
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48 <when value="cached">
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49 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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50 <options from_data_table="all_fasta">
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51 </options>
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52 <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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53 </param>
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54 </when>
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55 <when value="history">
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56 <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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57 </when>
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58 </conditional>
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59 <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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60 <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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61 <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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62 <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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63 <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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64 <option value="ALL_READS" selected="True">All reads</option>
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65 <option value="SAMPLE">Sample</option>
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66 <option value="LIBRARY">Library</option>
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67 <option value="READ_GROUP">Read group</option>
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68 </param>
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69
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70 <expand macro="VS" />
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71
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72 </inputs>
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73
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74 <outputs>
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75 <data format="tabular" name="outFile"/>
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76 <data format="pdf" name="histFile"/>
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77 </outputs>
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78
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79 <tests>
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80 <test>
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81 <param name="metric_accumulation_level" value="ALL_READS"/>
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82 <param name="deviations" value="10.0" />
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83 <param name="hist_width" value="500" />
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84 <param name="min_pct" value="0.05" />
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85 <param name="assume_sorted" value="true" />
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86 <param name="reference_source_selector" value="history" />
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87 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
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88 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
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89 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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90 </test>
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91 </tests>
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93
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94 <help>
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95
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96 .. class:: infomark
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97
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98 **Purpose**
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99
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100 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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101
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102 @dataset_collections@
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103
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104 @description@
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105
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106
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107 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
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108 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
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109 includes enough anomalous values from chimeras and other artifacts to make the mean and
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110 sd grossly misleading regarding the real distribution. Default value: 10.0.
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111
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112 HISTOGRAM_WIDTH=Integer
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113 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
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114 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
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115 included. Default value: not set.
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116
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117 MINIMUM_PCT=Float
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118 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
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119 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
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120
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121 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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122 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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123 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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124
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125 ASSUME_SORTED=Boolean
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126 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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127 value: true. This option can be set to 'null' to clear the default value. Possible
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128 values: {true, false}
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129
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130 @more_info@
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131
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132 </help>
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133 <expand macro="citations" />
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134 </tool>