Mercurial > repos > devteam > picard

annotate picard_QualityScoreDistribution.xml @ 24:b9fbec5ac6b2 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 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:52 -0400
parents 2a17c789e0a5
children f9242e01365a
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="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>chart quality score distribution</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">
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
8 <requirement type="package" version="3.4.1">r-base</requirement>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
9 </expand>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 ##set up input files
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 #set $reference_fasta_filename = "localref.fa"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
15
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
16 @handle_reference_source@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
17
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
18 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 QualityScoreDistribution
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
20 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 CHART_OUTPUT="${pdfFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 ALIGNED_READS_ONLY="${aligned_reads_only}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 PF_READS_ONLY="${pf_reads_only}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 INCLUDE_NO_CALLS="${include_no_calls}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 ASSUME_SORTED="${assume_sorted}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 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
33 @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
34
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
35 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <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
38 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <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
48 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <when value="history">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
58
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
60
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 </inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
62
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
67
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <param name="assume_sorted" value="true" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <param name="aligned_reads_only" value="false" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="pf_reads_only" value="false" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="include_no_calls" value="false" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
78 </test>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
80
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
81
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 Program to chart quality score distributions in a SAM or BAM dataset.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
94 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
95 false. Possible values: {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
97 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 Possible values: {true, false}
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
99
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
100 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
101 false. Possible values: {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 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
104 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
109 <expand macro="citations" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110 </tool>