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annotate picard_CollectSequencingArtifactsMetrics.xml @ 18:f8748e3fd865 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
author iuc
date Thu, 16 May 2019 07:12:56 -0400
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18
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
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1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>Collect metrics to quantify single-base sequencing artifacts</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
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14 #set $reference_fasta_filename = "localref.fa"
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15 @handle_reference_source@
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16
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17 picard
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18 CollectSequencingArtifactMetrics
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19 I='$escaped_element_identifier'
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20 O='OutPut'
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21 R='${reference_fasta_filename}'
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22 AS=${assume_sorted}
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23 CONTEXT_SIZE=${context_size}
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24 INCLUDE_DUPLICATES='${duplicates}'
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25 #if $contexts_to_print
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26 #for $context in str($contexts_to_print).split(','):
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27 CONTEXTS_TO_PRINT='${context}'
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28 #end for;
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29 #end if;
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30 MINIMUM_QUALITY_SCORE='${min_quality_score}'
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31 INCLUDE_UNPAIRED='${unpaired}'
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32 MAXIMUM_INSERT_SIZE='${max_size}'
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33 MINIMUM_INSERT_SIZE='${min_size}'
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34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
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35 ]]></command>
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36 <inputs>
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37 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
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38 <conditional name="reference_source">
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39 <param name="reference_source_selector" type="select" label="Load reference genome from">
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40 <option value="cached">Local cache</option>
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41 <option value="history">History</option>
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42 </param>
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43 <when value="cached">
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44 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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45 <options from_data_table="picard_indexes">
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46 <filter type="sort_by" column="2" />
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47 <validator type="no_options" message="No indexes are available" />
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48 </options>
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49 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
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50 </param>
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51 </when>
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52 <when value="history">
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53 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
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54 </when>
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55 </conditional>
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56
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57 <param name='context_size' value="1" type='integer' label='How many nucleotides (context) on each side to consider' help='e.g NXN corresponds to 1 "N" on each side of "X"'/>
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58 <param name="contexts_to_print" type="text" label="Contexts to print in the detailed tables, separated by comma (avoid spaces)" help="e.g. (for context size=1) AAA,AGG. Default prints all contexts">
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59 <sanitizer>
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60 <valid initial="string.letters"><add value="," /></valid>
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61 </sanitizer>
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62 </param>
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63 <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
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64 <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
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65 <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
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66 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
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67 <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
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68 <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
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69 <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>
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70
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71 <expand macro="VS" />
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73 </inputs>
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74
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75 <outputs>
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76 <data name='pre_details' format="tabular" from_work_dir="OutPut.pre_adapter_detail_metrics" label='Detailed table for artifacts introduced prior to the addition of adapters'/>
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77 <data name='pre_summary' format="tabular" from_work_dir="OutPut.pre_adapter_summary_metrics" label='Summary table for artifacts introduced prior to the addition of adapters'/>
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78 <data name='pos_details' format="tabular" from_work_dir="OutPut.bait_bias_detail_metrics" label='Detailed table for artifacts introduced posterior to the addition of adapters'/>
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79 <data name='pos_summary' format="tabular" from_work_dir="OutPut.bait_bias_summary_metrics" label='Summary table for artifacts introduced posterior to the addition of adapters'/>
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80 <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
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81 </outputs>
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82
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83 <tests>
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84 <test>
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85 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
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86 <param name="reference_source_selector" value="history"/>
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87 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
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88 <param name="context_size" value="1" />
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89 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
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90 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
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91 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
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92 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
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93 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
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94 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
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95 </test>
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96 <test>
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97 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
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98 <param name="reference_source_selector" value="cached"/>
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99 <param name="context_size" value="1" />
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100 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
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101 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
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102 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
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103 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
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104 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
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105 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
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106 </test>
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107 </tests>
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108 <help>
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109
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110 .. class:: infomark
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111
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112 **Purpose**
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113
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114 Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
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115
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116 @dataset_collections@
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117
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118 @description@
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119
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120 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored.
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121 Default: True
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122
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123 CONTEXT_SIZE=integer The number of context bases to include on each side of the assayed base.
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124
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125 CONTEXT_SIZE_TO_PRINT=String If specified, only print results for these contexts in the detail metrics output.
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126 However, the summary metrics output will still take all contexts into consideration.
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127
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128 DB_SNP=text file VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
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129
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130 INCLUDE_DUPLICATES=Boolean Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.
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131
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132 INCLUDE_UNPAIRED=Boolean Include unpaired reads. If set to true then all paired reads will be included as well -
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133 MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
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134
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135 MAXIMUM_INSERT_SIZE=Integer The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
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136 Default = 600
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137
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138 MINIMUM_INSERT_SIZE=Integer The minimum insert size for a read to be included in analysis. Default = 60
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139
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140 MINIMUM_MAPPING_QUALITY The minimum mapping quality score for a base to be included in analysis. Default = 30
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141
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142 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20
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143
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144 @more_info@
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145
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146 </help>
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147 <expand macro="citations" />
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148 </tool>