Mercurial > repos > devteam > picard
annotate picard_MeanQualityByCycle.xml @ 31:585027e65f3b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
author | iuc |
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date | Sat, 25 Feb 2023 20:33:49 +0000 |
parents | 2a17c789e0a5 |
children | f9242e01365a |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
5 | 2 <description>chart distribution of base qualities</description> |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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5 <token name="@WRAPPER_VERSION@">1</token> |
5 | 6 </macros> |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <expand macro="requirements"> |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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8 <requirement type="package" version="3.4.1">r-base</requirement> |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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9 </expand> |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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10 <command detect_errors="exit_code"><![CDATA[ |
5 | 11 @java_options@ |
12 ##set up input files | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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13 @symlink_element_identifier@ |
5 | 14 #set $reference_fasta_filename = "localref.fa" |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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15 |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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16 @handle_reference_source@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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17 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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18 picard |
5 | 19 MeanQualityByCycle |
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465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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20 INPUT='$escaped_element_identifier' |
5 | 21 OUTPUT="${outFile}" |
22 CHART_OUTPUT="${pdfFile}" | |
23 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
24 ALIGNED_READS_ONLY="${aligned_reads_only}" | |
25 PF_READS_ONLY="${pf_reads_only}" | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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26 |
5 | 27 ASSUME_SORTED="${assume_sorted}" |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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28 |
5 | 29 VALIDATION_STRINGENCY="${validation_stringency}" |
30 QUIET=true | |
31 VERBOSITY=ERROR | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
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32 @TMPDIR_OPTION@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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33 |
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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34 ]]></command> |
5 | 35 <inputs> |
36 <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."/> | |
37 <conditional name="reference_source"> | |
38 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
39 <option value="cached">Local cache</option> | |
40 <option value="history">History</option> | |
41 </param> | |
42 <when value="cached"> | |
43 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
44 <options from_data_table="all_fasta"> | |
45 </options> | |
46 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
47 </param> | |
48 </when> | |
49 <when value="history"> | |
50 <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" /> | |
51 </when> | |
52 </conditional> | |
53 <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"/> | |
54 <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"/> | |
55 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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56 |
5 | 57 <expand macro="VS" /> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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58 |
5 | 59 </inputs> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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60 |
5 | 61 <outputs> |
62 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
63 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> | |
64 </outputs> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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65 |
5 | 66 <tests> |
67 <test> | |
68 <param name="assume_sorted" value="true" /> | |
69 <param name="aligned_reads_only" value="false" /> | |
70 <param name="pf_reads_only" value="false" /> | |
71 <param name="reference_source_selector" value="history" /> | |
72 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> | |
73 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> | |
74 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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75 </test> |
5 | 76 </tests> |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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77 |
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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78 |
5 | 79 <help> |
80 | |
81 .. class:: infomark | |
82 | |
83 **Purpose** | |
84 | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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85 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. |
5 | 86 |
87 @dataset_collections@ | |
88 | |
89 @description@ | |
90 | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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91 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
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92 false. Possible values: {true, false} |
5 | 93 |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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94 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
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95 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
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96 false} |
5 | 97 |
98 ASSUME_SORTED=Boolean | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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99 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True |
5 | 100 |
101 @more_info@ | |
102 | |
103 </help> | |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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104 <expand macro="citations" /> |
5 | 105 </tool> |