Mercurial > repos > devteam > picard

annotate picard_CollectAlignmentSummaryMetrics.xml @ 29:1aac2a13842a draft

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 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:06:40 +0000
parents 2a17c789e0a5
children 585027e65f3b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>writes a file containing summary alignment metrics</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
7 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 10
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
10 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 ##set up input files
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 #set $reference_fasta_filename = "localref.fa"
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
14
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
15 @handle_reference_source@
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
16
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 10
diff changeset
17 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 CollectAlignmentSummaryMetrics
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
19 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 MAX_INSERT_SIZE=${maxinsert}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 #for $sequence in $adapters:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 ADAPTER_SEQUENCE="${sequence.adapter}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 #end for
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
25 #for $level in str($metric_accumulation_level).split(','):
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
26 METRIC_ACCUMULATION_LEVEL="${level}"
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
27 #end for
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 IS_BISULFITE_SEQUENCED="${bisulphite}"
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
29
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 REFERENCE_SEQUENCE="${reference_fasta_filename}"
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
31
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 ASSUME_SORTED="${assume_sorted}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 VERBOSITY=ERROR
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
37 @TMPDIR_OPTION@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
38
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 10
diff changeset
39 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 <when value="history">
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
55 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 <option value="ALL_READS" selected="True">All reads</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 <option value="SAMPLE">Sample</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 <option value="LIBRARY">Library</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <option value="READ_GROUP">Read group</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
67 <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 </repeat>
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
69 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <expand macro="VS" />
10
777ccdd1d6e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents: 9
diff changeset
71
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <param name="bisulphite" value="false" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 <param name="sorted" value="true" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <param name="adaptors" value="" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <param name="maxinsert" value="100000" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 <param name="ref_file" value="picard_CASM_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 Reads a SAM or BAM file and writes a file containing summary alignment metrics.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
100 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
101 inter-chromosomal pairs. Default value: 100000.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
103 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
104 be specified 0 or more times.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
107 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
108 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
109
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110 IS_BISULFITE_SEQUENCED=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
111 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
112
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
113
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
114 REFERENCE_SEQUENCE=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
115 R=File Reference sequence fasta Default value: null.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
116
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
117 ASSUME_SORTED=Boolean
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
118 AS=Boolean If true (default), then the sort order in the header file will be ignored.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
119
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
120 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
121
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
122 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
123 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
124 </tool>