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comparison picard_CollectSequencingArtifactsMetrics.xml @ 23:1cd1cf786389 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 07:13:32 -0400
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children b502c227b5e6
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22:f6ced08779c4 23:1cd1cf786389
1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
2 <description>Collect metrics to quantify single-base sequencing artifacts</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package" version="3.4.1">r-base</requirement>
9 </expand>
10 <command detect_errors="exit_code"><![CDATA[
11 @java_options@
12 @symlink_element_identifier@
13
14 #set $reference_fasta_filename = "localref.fa"
15 @handle_reference_source@
16
17 picard
18 CollectSequencingArtifactMetrics
19 I='$escaped_element_identifier'
20 O='OutPut'
21 R='${reference_fasta_filename}'
22 AS=${assume_sorted}
23 CONTEXT_SIZE=${context_size}
24 INCLUDE_DUPLICATES='${duplicates}'
25 #if $contexts_to_print
26 #for $context in str($contexts_to_print).split(','):
27 CONTEXTS_TO_PRINT='${context}'
28 #end for;
29 #end if;
30 MINIMUM_QUALITY_SCORE='${min_quality_score}'
31 INCLUDE_UNPAIRED='${unpaired}'
32 MAXIMUM_INSERT_SIZE='${max_size}'
33 MINIMUM_INSERT_SIZE='${min_size}'
34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
35 ]]></command>
36 <inputs>
37 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
38 <conditional name="reference_source">
39 <param name="reference_source_selector" type="select" label="Load reference genome from">
40 <option value="cached">Local cache</option>
41 <option value="history">History</option>
42 </param>
43 <when value="cached">
44 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
45 <options from_data_table="picard_indexes">
46 <filter type="sort_by" column="2" />
47 <validator type="no_options" message="No indexes are available" />
48 </options>
49 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
50 </param>
51 </when>
52 <when value="history">
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" />
54 </when>
55 </conditional>
56
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"'/>
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">
59 <sanitizer>
60 <valid initial="string.letters"><add value="," /></valid>
61 </sanitizer>
62 </param>
63 <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
64 <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
65 <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
66 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
67 <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
68 <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
69 <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>
70
71 <expand macro="VS" />
72
73 </inputs>
74
75 <outputs>
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'/>
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'/>
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'/>
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'/>
80 <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
81 </outputs>
82
83 <tests>
84 <test>
85 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
86 <param name="reference_source_selector" value="history"/>
87 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
88 <param name="context_size" value="1" />
89 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
90 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
91 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
92 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
93 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
94 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
95 </test>
96 <test>
97 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
98 <param name="reference_source_selector" value="cached"/>
99 <param name="context_size" value="1" />
100 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
101 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
102 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
103 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
104 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
105 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
106 </test>
107 </tests>
108 <help>
109
110 .. class:: infomark
111
112 **Purpose**
113
114 Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
115
116 @dataset_collections@
117
118 @description@
119
120 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored.
121 Default: True
122
123 CONTEXT_SIZE=integer The number of context bases to include on each side of the assayed base.
124
125 CONTEXT_SIZE_TO_PRINT=String If specified, only print results for these contexts in the detail metrics output.
126 However, the summary metrics output will still take all contexts into consideration.
127
128 DB_SNP=text file VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
129
130 INCLUDE_DUPLICATES=Boolean Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.
131
132 INCLUDE_UNPAIRED=Boolean Include unpaired reads. If set to true then all paired reads will be included as well -
133 MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
134
135 MAXIMUM_INSERT_SIZE=Integer The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
136 Default = 600
137
138 MINIMUM_INSERT_SIZE=Integer The minimum insert size for a read to be included in analysis. Default = 60
139
140 MINIMUM_MAPPING_QUALITY The minimum mapping quality score for a base to be included in analysis. Default = 30
141
142 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20
143
144 @more_info@
145
146 </help>
147 <expand macro="citations" />
148 </tool>