Mercurial > repos > devteam > picard

annotate picard_MeanQualityByCycle.xml @ 13:7e6fd3d0f16e 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-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>chart distribution of base qualities</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </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
6 <expand macro="requirements">
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
7 <requirement type="package" version="3.3.1">r</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
8 </expand>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 ##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
12 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 #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
14
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #if str( $reference_source.reference_source_selector ) == "history":
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 #else:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
20
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
21 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 MeanQualityByCycle
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
23 INPUT='$inputFile.element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 CHART_OUTPUT="${pdfFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 ALIGNED_READS_ONLY="${aligned_reads_only}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 PF_READS_ONLY="${pf_reads_only}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
29
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 ASSUME_SORTED="${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
31
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
35
12
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="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="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
56 <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
57 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="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
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="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <output name="outFile" file="picard_MeanQualityByCycle_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
77 </test>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
79
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
80
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
87 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
93 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
94 false. Possible values: {true, false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
96 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
97 This option can be set to 'null' to clear the default value. Possible values: {true,
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
98 false}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 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
101 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
102
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108