Mercurial > repos > devteam > picard
comparison picard_CollectSequencingArtifactsMetrics.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author | iuc |
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date | Sun, 03 Mar 2024 16:06:11 +0000 |
parents | b502c227b5e6 |
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32:f9242e01365a | 33:3f254c5ced1d |
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1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool id="picard_artifact_metrics" name="Picard Collect Sequencing Artifact Metrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> |
2 <description>Collect metrics to quantify single-base sequencing artifacts</description> | 2 <description>Collect metrics to quantify single-base sequencing artifacts</description> |
3 <macros> | 3 <macros> |
4 <import>picard_macros.xml</import> | 4 <import>picard_macros.xml</import> |
5 <token name="@WRAPPER_VERSION@">2</token> | 5 <token name="@WRAPPER_VERSION@">0</token> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
8 <requirement type="package" version="3.4.1">r-base</requirement> | |
9 </expand> | 8 </expand> |
10 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
11 @java_options@ | 10 @java_options@ |
12 @symlink_element_identifier@ | 11 @symlink_element_identifier@ |
13 | 12 |
14 #set $reference_fasta_filename = "localref.fa" | 13 #set $reference_fasta_filename = "localref.fa" |
15 @handle_reference_source@ | 14 @handle_reference_source@ |
16 | 15 |
17 picard | 16 picard CollectSequencingArtifactMetrics |
18 CollectSequencingArtifactMetrics | 17 --I '$escaped_element_identifier' |
19 I='$escaped_element_identifier' | 18 --O 'OutPut' |
20 O='OutPut' | 19 --R '${reference_fasta_filename}' |
21 R='${reference_fasta_filename}' | 20 --AS ${assume_sorted} |
22 AS=${assume_sorted} | 21 --CONTEXT_SIZE ${context_size} |
23 CONTEXT_SIZE=${context_size} | 22 --INCLUDE_DUPLICATES '${duplicates}' |
24 INCLUDE_DUPLICATES='${duplicates}' | |
25 #if $contexts_to_print | 23 #if $contexts_to_print |
26 #for $context in str($contexts_to_print).split(','): | 24 #for $context in str($contexts_to_print).split(','): |
27 CONTEXTS_TO_PRINT='${context}' | 25 --CONTEXTS_TO_PRINT '${context}' |
28 #end for; | 26 #end for; |
29 #end if; | 27 #end if; |
30 MINIMUM_QUALITY_SCORE='${min_quality_score}' | 28 --MINIMUM_QUALITY_SCORE '${min_quality_score}' |
31 INCLUDE_UNPAIRED='${unpaired}' | 29 --INCLUDE_UNPAIRED '${unpaired}' |
32 MAXIMUM_INSERT_SIZE='${max_size}' | 30 --MAXIMUM_INSERT_SIZE '${max_size}' |
33 MINIMUM_INSERT_SIZE='${min_size}' | 31 --MINIMUM_INSERT_SIZE '${min_size}' |
34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}' | 32 --MINIMUM_MAPPING_QUALITY '${minim_map_quality}' |
35 VALIDATION_STRINGENCY='${validation_stringency}'; | 33 --VALIDATION_STRINGENCY '${validation_stringency}'; |
36 ]]></command> | 34 ]]></command> |
37 <inputs> | 35 <inputs> |
38 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/> | 36 <param name="inputFile" format="sam,bam" type="data" label="SAM/BAM Input file"/> |
39 <conditional name="reference_source"> | 37 <conditional name="reference_source"> |
40 <param name="reference_source_selector" type="select" label="Load reference genome from"> | 38 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
41 <option value="cached">Local cache</option> | 39 <option value="cached">Local cache</option> |
42 <option value="history">History</option> | 40 <option value="history">History</option> |
43 </param> | 41 </param> |
44 <when value="cached"> | 42 <when value="cached"> |
45 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> | 43 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> |
46 <options from_data_table="picard_indexes"> | 44 <options from_data_table="picard_indexes"> |
47 <filter type="sort_by" column="2" /> | 45 <filter type="sort_by" column="2"/> |
48 <validator type="no_options" message="No indexes are available" /> | 46 <validator type="no_options" message="No indexes are available"/> |
49 </options> | 47 </options> |
50 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> | 48 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> |
49 </param> | |
50 </when> | |
51 <when value="history"> | |
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"/> | |
53 </when> | |
54 </conditional> | |
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 "N" on each side of "X""/> | |
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"> | |
57 <sanitizer> | |
58 <valid initial="string.letters"> | |
59 <add value=","/> | |
60 </valid> | |
61 </sanitizer> | |
51 </param> | 62 </param> |
52 </when> | 63 <param name="min_quality_score" type="integer" value="30" label="Minimum base quality score"/> |
53 <when value="history"> | 64 <param name="max_size" type="integer" value="600" label="Maximum insert size"/> |
54 <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" /> | 65 <param name="min_size" type="integer" value="30" label="Minimum insert size"/> |
55 </when> | 66 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/> |
56 </conditional> | 67 <param name="assume_sorted" type="boolean" label="Assume SAM/BAM is sorted"/> |
57 | 68 <param name="duplicates" type="boolean" label="Include duplicates" checked="false" truevalue="true" falsevalue="false"/> |
58 <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"'/> | 69 <param name="unpaired" type="boolean" label="Include unpaired reads" checked="false" truevalue="true" falsevalue="false"/> |
59 <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"> | 70 <expand macro="VS"/> |
60 <sanitizer> | 71 </inputs> |
61 <valid initial="string.letters"><add value="," /></valid> | 72 <outputs> |
62 </sanitizer> | 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"/> |
63 </param> | 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"/> |
64 <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/> | 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"/> |
65 <param name="max_size" type="integer" value="600" label="Maximum insert size"/> | 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"/> |
66 <param name="min_size" type="integer" value="30" label="Minimum insert size"/> | 77 <data name="err_summary" format="tabular" from_work_dir="OutPut.error_summary_metrics" label="General Summary of artifactual errors"/> |
67 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/> | 78 </outputs> |
68 <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/> | 79 <tests> |
69 <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/> | 80 <test> |
70 <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/> | 81 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam"/> |
71 | 82 <param name="reference_source_selector" value="history"/> |
72 <expand macro="VS" /> | 83 <param name="ref_file" value="picard_BedToIntervalList_ref.fa"/> |
73 | 84 <param name="context_size" value="1"/> |
74 </inputs> | 85 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/> |
75 | 86 <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/> |
76 <outputs> | 87 <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/> |
77 <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'/> | 88 <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/> |
78 <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'/> | 89 <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/> |
79 <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'/> | 90 <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/> |
80 <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'/> | 91 </test> |
81 <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/> | 92 <test> |
82 </outputs> | 93 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/> |
83 | 94 <param name="reference_source_selector" value="cached"/> |
84 <tests> | 95 <param name="context_size" value="1"/> |
85 <test> | 96 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG"/> |
86 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" /> | 97 <output name="pre_details" file="pre_details" ftype="tabular" value="pre_detail" lines_diff="4"/> |
87 <param name="reference_source_selector" value="history"/> | 98 <output name="pre_summary" file="pre_summary" ftype="tabular" value="pre_summary" lines_diff="4"/> |
88 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" /> | 99 <output name="pos_details" file="pos_details" ftype="tabular" value="pos_detail" lines_diff="4"/> |
89 <param name="context_size" value="1" /> | 100 <output name="pos_summary" file="pos_summary" ftype="tabular" value="pos_summary" lines_diff="4"/> |
90 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" /> | 101 <output name="err_summary" file="err_summary" ftype="tabular" value="err_summary" lines_diff="4"/> |
91 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/> | 102 </test> |
92 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/> | 103 </tests> |
93 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/> | 104 <help> |
94 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/> | |
95 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/> | |
96 </test> | |
97 <test> | |
98 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/> | |
99 <param name="reference_source_selector" value="cached"/> | |
100 <param name="context_size" value="1" /> | |
101 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" /> | |
102 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/> | |
103 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/> | |
104 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/> | |
105 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/> | |
106 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/> | |
107 </test> | |
108 </tests> | |
109 <help> | |
110 | 105 |
111 .. class:: infomark | 106 .. class:: infomark |
112 | 107 |
113 **Purpose** | 108 **Purpose** |
114 | 109 |
143 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20 | 138 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20 |
144 | 139 |
145 @more_info@ | 140 @more_info@ |
146 | 141 |
147 </help> | 142 </help> |
148 <expand macro="citations" /> | 143 <expand macro="citations"/> |
149 </tool> | 144 </tool> |