Mercurial > repos > devteam > picard

annotate picard_CollectSequencingArtifactsMetrics.xml @ 28:c943f4a04af0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:31:14 +0000
parents fc3866ddc7b6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
1 <tool id='picard_artifact_metrics' name='Picard Collect Sequencing Artifact Metrics' version="@TOOL_VERSION@.@WRAPPER_VERSION@">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
2 <description>Collect metrics to quantify single-base sequencing artifacts</description>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
3 <macros>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
4 <import>picard_macros.xml</import>
26
fc3866ddc7b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
iuc
parents: 18
diff changeset
5 <token name="@WRAPPER_VERSION@">2</token>
18
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
6 </macros>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
7 <expand macro="requirements">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
8 <requirement type="package" version="3.4.1">r-base</requirement>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
9 </expand>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
11 @java_options@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
12 @symlink_element_identifier@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
13
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
14 #set $reference_fasta_filename = "localref.fa"
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
15 @handle_reference_source@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
16
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
17 picard
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
18 CollectSequencingArtifactMetrics
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
19 I='$escaped_element_identifier'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
20 O='OutPut'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
21 R='${reference_fasta_filename}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
22 AS=${assume_sorted}
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
23 CONTEXT_SIZE=${context_size}
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
24 INCLUDE_DUPLICATES='${duplicates}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
25 #if $contexts_to_print
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
26 #for $context in str($contexts_to_print).split(','):
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
27 CONTEXTS_TO_PRINT='${context}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
28 #end for;
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
29 #end if;
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
30 MINIMUM_QUALITY_SCORE='${min_quality_score}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
31 INCLUDE_UNPAIRED='${unpaired}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
32 MAXIMUM_INSERT_SIZE='${max_size}'
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
33 MINIMUM_INSERT_SIZE='${min_size}'
26
fc3866ddc7b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
iuc
parents: 18
diff changeset
34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}'
fc3866ddc7b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
iuc
parents: 18
diff changeset
35 VALIDATION_STRINGENCY='${validation_stringency}';
18
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
36 ]]></command>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
37 <inputs>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
38 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
39 <conditional name="reference_source">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
40 <param name="reference_source_selector" type="select" label="Load reference genome from">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
41 <option value="cached">Local cache</option>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
42 <option value="history">History</option>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
43 </param>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
44 <when value="cached">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
45 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
46 <options from_data_table="picard_indexes">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
47 <filter type="sort_by" column="2" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
48 <validator type="no_options" message="No indexes are available" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
49 </options>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
50 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
51 </param>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
52 </when>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
53 <when value="history">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
55 </when>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
56 </conditional>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
57
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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"'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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">
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
60 <sanitizer>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
61 <valid initial="string.letters"><add value="," /></valid>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
62 </sanitizer>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
63 </param>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
64 <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
65 <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
66 <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
67 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
68 <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
69 <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
70 <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
71
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
72 <expand macro="VS" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
73
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
74 </inputs>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
75
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
76 <outputs>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
81 <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
82 </outputs>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
83
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
84 <tests>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
85 <test>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
86 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
87 <param name="reference_source_selector" value="history"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
88 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
89 <param name="context_size" value="1" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
90 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
91 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
92 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
93 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
94 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
95 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
96 </test>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
97 <test>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
98 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
99 <param name="reference_source_selector" value="cached"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
100 <param name="context_size" value="1" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
101 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
102 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
103 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
104 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
105 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
106 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
107 </test>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
108 </tests>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
109 <help>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
110
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
111 .. class:: infomark
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
112
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
113 **Purpose**
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
114
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
115 Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
116
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
117 @dataset_collections@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
118
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
119 @description@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
120
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
121 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
122 Default: True
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
123
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
124 CONTEXT_SIZE=integer The number of context bases to include on each side of the assayed base.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
125
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
126 CONTEXT_SIZE_TO_PRINT=String If specified, only print results for these contexts in the detail metrics output.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
127 However, the summary metrics output will still take all contexts into consideration.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
128
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
129 DB_SNP=text file VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
130
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
131 INCLUDE_DUPLICATES=Boolean Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
132
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
133 INCLUDE_UNPAIRED=Boolean Include unpaired reads. If set to true then all paired reads will be included as well -
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
134 MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
135
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
136 MAXIMUM_INSERT_SIZE=Integer The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
137 Default = 600
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
138
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
139 MINIMUM_INSERT_SIZE=Integer The minimum insert size for a read to be included in analysis. Default = 60
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
140
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
141 MINIMUM_MAPPING_QUALITY The minimum mapping quality score for a base to be included in analysis. Default = 30
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
142
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
143 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
144
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
145 @more_info@
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
146
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
147 </help>
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
148 <expand macro="citations" />
f8748e3fd865 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
149 </tool>