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annotate picard_CollectInsertSizeMetrics.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
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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 ##set up input files
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13 #set $reference_fasta_filename = "localref.fa"
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15 #if str( $reference_source.reference_source_selector ) == "history":
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16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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17 #else:
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18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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19 #end if
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21 picard
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22 CollectInsertSizeMetrics
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23 INPUT="${inputFile}"
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24 OUTPUT="${outFile}"
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25 HISTOGRAM_FILE="${histFile}"
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26 DEVIATIONS="${deviations}"
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28 #if str( $hist_width ):
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29 HISTOGRAM_WIDTH="${hist_width}"
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30 #end if
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32 MINIMUM_PCT="${min_pct}"
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33 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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34 ASSUME_SORTED="${assume_sorted}"
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35 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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37 VALIDATION_STRINGENCY="${validation_stringency}"
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38 QUIET=true
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39 VERBOSITY=ERROR
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40
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41 ]]></command>
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42 <inputs>
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43 <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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44 <conditional name="reference_source">
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45 <param name="reference_source_selector" type="select" label="Load reference genome from">
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46 <option value="cached">Local cache</option>
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47 <option value="history">History</option>
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48 </param>
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49 <when value="cached">
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50 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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51 <options from_data_table="all_fasta">
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52 </options>
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53 <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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54 </param>
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55 </when>
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56 <when value="history">
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57 <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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58 </when>
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59 </conditional>
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60 <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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61 <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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62 <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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63 <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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64 <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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65 <option value="ALL_READS" selected="True">All reads</option>
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66 <option value="SAMPLE">Sample</option>
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67 <option value="LIBRARY">Library</option>
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68 <option value="READ_GROUP">Read group</option>
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69 </param>
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71 <expand macro="VS" />
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73 </inputs>
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75 <outputs>
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76 <data format="tabular" name="outFile"/>
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77 <data format="pdf" name="histFile"/>
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78 </outputs>
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80 <tests>
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81 <test>
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82 <param name="metric_accumulation_level" value="ALL_READS"/>
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83 <param name="deviations" value="10.0" />
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84 <param name="hist_width" value="500" />
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85 <param name="min_pct" value="0.05" />
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86 <param name="assume_sorted" value="true" />
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87 <param name="reference_source_selector" value="history" />
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88 <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
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89 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
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90 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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91 </test>
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92 </tests>
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93
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94
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95 <help>
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96
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97 .. class:: infomark
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98
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99 **Purpose**
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100
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101 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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102
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103 @dataset_collections@
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104
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105 @description@
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106
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107
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108 DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN +
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109 DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
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110 includes enough anomalous values from chimeras and other artifacts to make the mean and
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111 sd grossly misleading regarding the real distribution. Default value: 10.0.
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112
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113 HISTOGRAM_WIDTH=Integer
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114 W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
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115 Also, when calculating mean and standard deviation, only bins &lt;= Histogram_WIDTH will be
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116 included. Default value: not set.
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117
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118 MINIMUM_PCT=Float
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119 M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
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120 have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05.
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121
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122 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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123 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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124 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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125
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126 ASSUME_SORTED=Boolean
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127 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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128 value: true. This option can be set to 'null' to clear the default value. Possible
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129 values: {true, false}
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130
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131 @more_info@
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132
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133 </help>
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134 </tool>
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135
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136