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annotate picard_CollectSequencingArtifactsMetrics.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents b502c227b5e6
children
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1 <tool id="picard_artifact_metrics" name="Picard Collect Sequencing Artifact Metrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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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@">0</token>
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6 </macros>
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7 <expand macro="requirements">
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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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13 #set $reference_fasta_filename = "localref.fa"
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14 @handle_reference_source@
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15
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16 picard CollectSequencingArtifactMetrics
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17 --I '$escaped_element_identifier'
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18 --O 'OutPut'
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19 --R '${reference_fasta_filename}'
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20 --AS ${assume_sorted}
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21 --CONTEXT_SIZE ${context_size}
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22 --INCLUDE_DUPLICATES '${duplicates}'
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23 #if $contexts_to_print
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24 #for $context in str($contexts_to_print).split(','):
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25 --CONTEXTS_TO_PRINT '${context}'
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26 #end for;
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27 #end if;
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28 --MINIMUM_QUALITY_SCORE '${min_quality_score}'
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29 --INCLUDE_UNPAIRED '${unpaired}'
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30 --MAXIMUM_INSERT_SIZE '${max_size}'
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31 --MINIMUM_INSERT_SIZE '${min_size}'
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32 --MINIMUM_MAPPING_QUALITY '${minim_map_quality}'
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33 --VALIDATION_STRINGENCY '${validation_stringency}';
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34 ]]></command>
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35 <inputs>
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36 <param name="inputFile" format="sam,bam" type="data" label="SAM/BAM Input file"/>
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37 <conditional name="reference_source">
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38 <param name="reference_source_selector" type="select" label="Load reference genome from">
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39 <option value="cached">Local cache</option>
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40 <option value="history">History</option>
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41 </param>
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42 <when value="cached">
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43 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
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44 <options from_data_table="picard_indexes">
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45 <filter type="sort_by" column="2"/>
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46 <validator type="no_options" message="No indexes are available"/>
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47 </options>
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48 <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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49 </param>
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50 </when>
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51 <when value="history">
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52 <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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53 </when>
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54 </conditional>
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55 <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 &quot;N&quot; on each side of &quot;X&quot;"/>
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56 <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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57 <sanitizer>
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58 <valid initial="string.letters">
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59 <add value=","/>
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60 </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 <expand macro="VS"/>
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71 </inputs>
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72 <outputs>
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73 <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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74 <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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75 <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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76 <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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77 <data name="err_summary" format="tabular" from_work_dir="OutPut.error_summary_metrics" label="General Summary of artifactual errors"/>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam"/>
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82 <param name="reference_source_selector" value="history"/>
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83 <param name="ref_file" value="picard_BedToIntervalList_ref.fa"/>
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84 <param name="context_size" value="1"/>
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85 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/>
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86 <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/>
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87 <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/>
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88 <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/>
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89 <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/>
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90 <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/>
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91 </test>
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92 <test>
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93 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
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94 <param name="reference_source_selector" value="cached"/>
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95 <param name="context_size" value="1"/>
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96 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/>
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97 <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/>
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98 <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/>
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99 <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/>
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100 <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/>
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101 <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/>
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102 </test>
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103 </tests>
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104 <help>
23
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105
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106 .. class:: infomark
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107
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108 **Purpose**
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109
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110 Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
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111
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112 @dataset_collections@
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113
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114 @description@
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115
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116 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored.
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117 Default: True
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118
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119 CONTEXT_SIZE=integer The number of context bases to include on each side of the assayed base.
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120
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121 CONTEXT_SIZE_TO_PRINT=String If specified, only print results for these contexts in the detail metrics output.
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122 However, the summary metrics output will still take all contexts into consideration.
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123
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124 DB_SNP=text file VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
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125
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126 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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127
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128 INCLUDE_UNPAIRED=Boolean Include unpaired reads. If set to true then all paired reads will be included as well -
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129 MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
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130
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131 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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132 Default = 600
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133
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134 MINIMUM_INSERT_SIZE=Integer The minimum insert size for a read to be included in analysis. Default = 60
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135
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136 MINIMUM_MAPPING_QUALITY The minimum mapping quality score for a base to be included in analysis. Default = 30
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137
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138 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20
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139
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140 @more_info@
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141
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142 </help>
33
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143 <expand macro="citations"/>
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144 </tool>