annotate picard_CollectSequencingArtifactsMetrics.xml @ 24:b9fbec5ac6b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:52 -0400
parents 1cd1cf786389
children b502c227b5e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
1cd1cf786389 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@">
1cd1cf786389 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>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
3 <macros>
1cd1cf786389 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>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
6 </macros>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
7 <expand macro="requirements">
1cd1cf786389 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>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
9 </expand>
1cd1cf786389 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[
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
11 @java_options@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
12 @symlink_element_identifier@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
13
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
14 #set $reference_fasta_filename = "localref.fa"
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
15 @handle_reference_source@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
16
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
17 picard
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
18 CollectSequencingArtifactMetrics
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
19 I='$escaped_element_identifier'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
20 O='OutPut'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
21 R='${reference_fasta_filename}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
22 AS=${assume_sorted}
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
23 CONTEXT_SIZE=${context_size}
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
24 INCLUDE_DUPLICATES='${duplicates}'
1cd1cf786389 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
1cd1cf786389 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(','):
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
27 CONTEXTS_TO_PRINT='${context}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
28 #end for;
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
29 #end if;
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
30 MINIMUM_QUALITY_SCORE='${min_quality_score}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
31 INCLUDE_UNPAIRED='${unpaired}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
32 MAXIMUM_INSERT_SIZE='${max_size}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
33 MINIMUM_INSERT_SIZE='${min_size}'
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
34 MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
35 ]]></command>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
36 <inputs>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
37 <param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
38 <conditional name="reference_source">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
39 <param name="reference_source_selector" type="select" label="Load reference genome from">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
40 <option value="cached">Local cache</option>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
41 <option value="history">History</option>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
42 </param>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
43 <when value="cached">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
44 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
45 <options from_data_table="picard_indexes">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
46 <filter type="sort_by" column="2" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
47 <validator type="no_options" message="No indexes are available" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
48 </options>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
49 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
50 </param>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
51 </when>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
52 <when value="history">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
54 </when>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
55 </conditional>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
56
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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"'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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">
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
59 <sanitizer>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
60 <valid initial="string.letters"><add value="," /></valid>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
61 </sanitizer>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
62 </param>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
63 <param name='min_quality_score' type='integer' value='30' label='Minimum base quality score'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
64 <param name="max_size" type="integer" value="600" label="Maximum insert size"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
65 <param name="min_size" type="integer" value="30" label="Minimum insert size"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
66 <param name="minim_map_quality" type="integer" value="20" label="Minimum mapping quality"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
67 <param name='assume_sorted' type='boolean' label='Assume SAM/BAM is sorted'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
68 <param name='duplicates' type='boolean' label='Include duplicates' checked="false" truevalue="true" falsevalue="false"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
69 <param name='unpaired' type='boolean' label='Include unpaired reads' checked="false" truevalue="true" falsevalue="false"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
70
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
71 <expand macro="VS" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
72
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
73 </inputs>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
74
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
75 <outputs>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
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'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
80 <data name='err_summary' format="tabular" from_work_dir="OutPut.error_summary_metrics" label='General Summary of artifactual errors'/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
81 </outputs>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
82
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
83 <tests>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
84 <test>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
85 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
86 <param name="reference_source_selector" value="history"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
87 <param name="ref_file" value="picard_BedToIntervalList_ref.fa" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
88 <param name="context_size" value="1" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
89 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
90 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
91 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
92 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
93 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
94 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
95 </test>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
96 <test>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
97 <param name="inputFile" value="picard_ARRG_test1.bam" ftype="bam" dbkey="hg38"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
98 <param name="reference_source_selector" value="cached"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
99 <param name="context_size" value="1" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
100 <param name="contexts_to_print" value="AAA,CAA,AAC,AAT,AAG" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
101 <output name='pre_details' file='pre_details' ftype="tabular" value="pre_detail" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
102 <output name='pre_summary' file='pre_summary' ftype="tabular" value="pre_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
103 <output name='pos_details' file='pos_details' ftype="tabular" value="pos_detail" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
104 <output name='pos_summary' file='pos_summary' ftype="tabular" value="pos_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
105 <output name='err_summary' file='err_summary' ftype="tabular" value="err_summary" lines_diff="4"/>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
106 </test>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
107 </tests>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
108 <help>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
109
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
110 .. class:: infomark
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
111
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
112 **Purpose**
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
113
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
114 Program to chart the distribution of potential sequencing "single nucleotide mutation" artifacts in a SAM or BAM file.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
115
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
116 @dataset_collections@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
117
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
118 @description@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
119
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
120 ASSUME_SORTED=Boolean If true (default), then the sort order in the header file will be ignored.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
121 Default: True
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
122
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
123 CONTEXT_SIZE=integer The number of context bases to include on each side of the assayed base.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
124
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
125 CONTEXT_SIZE_TO_PRINT=String If specified, only print results for these contexts in the detail metrics output.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
126 However, the summary metrics output will still take all contexts into consideration.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
127
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
128 DB_SNP=text file VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
129
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
130 INCLUDE_DUPLICATES=Boolean Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
131
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
132 INCLUDE_UNPAIRED=Boolean Include unpaired reads. If set to true then all paired reads will be included as well -
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
133 MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
134
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
135 MAXIMUM_INSERT_SIZE=Integer The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
136 Default = 600
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
137
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
138 MINIMUM_INSERT_SIZE=Integer The minimum insert size for a read to be included in analysis. Default = 60
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
139
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
140 MINIMUM_MAPPING_QUALITY The minimum mapping quality score for a base to be included in analysis. Default = 30
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
141
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
142 MINIMUM_QUALITY_SCORE The minimum base quality score for a base to be included in analysis. Default = 20
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
143
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
144 @more_info@
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
145
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
146 </help>
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
147 <expand macro="citations" />
1cd1cf786389 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ac1d8d6202e71ccfeaae7a4c36de3eb5a7ab582
iuc
parents:
diff changeset
148 </tool>