annotate picard_CollectGcBiasMetrics.xml @ 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b
author iuc
date Tue, 11 Jun 2019 02:36:54 -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="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>charts the GC bias 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">
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@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
12 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 ##set up input files
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #set $reference_fasta_filename = "localref.fa"
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
16
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
17 @handle_reference_source@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
18
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
19 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 CollectGcBiasMetrics
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
21 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 CHART_OUTPUT="${pdfFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 SUMMARY_OUTPUT="${summaryFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 WINDOW_SIZE="${window_size}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 ASSUME_SORTED="${assume_sorted}"
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
30
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 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
34 @TMPDIR_OPTION@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
35
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
36 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <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
39 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <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
49 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <when value="history">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 <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
53 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
57 <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
59
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 <expand macro="VS" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
61
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 </inputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
63
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 </outputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
69
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="window_size" value="100" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="minimum_genome_fraction" value="0.00005" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="assume_sorted" value="true" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="is_bisulfite_sequenced" value="true" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
80 </test>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 </tests>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
82
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
83
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 Program to chart the nucleotide distribution per cycle in a SAM or BAM file.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
96 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
97 false. Possible values: {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
100 This option can be set to 'null' to clear the default value. Possible values: {true,
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
101 false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 ASSUME_SORTED=Boolean
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
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>