Mercurial > repos > devteam > picard
annotate picard_CollectWgsMetrics.xml @ 21:6f9c0884a3e7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
| author | iuc |
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| date | Tue, 16 Oct 2018 11:49:10 -0400 |
| parents | 2a17c789e0a5 |
| children | f9242e01365a |
| rev | line source |
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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="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 5 | 2 <description>compute metrics for evaluating of whole genome sequencing experiments</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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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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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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8 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 9 @java_options@ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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10 @symlink_element_identifier@ |
| 5 | 11 ##set up input files |
| 12 | |
| 13 #set $reference_fasta_filename = "localref.fa" | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
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15 @handle_reference_source@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
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17 picard |
| 5 | 18 CollectWgsMetrics |
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465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
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19 INPUT='$escaped_element_identifier' |
| 5 | 20 OUTPUT="${outFile}" |
| 21 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 22 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" | |
| 23 MINIMUM_BASE_QUALITY="${minimum_base_quality}" | |
| 24 COVERAGE_CAP="${coverage_cap}" | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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25 |
| 5 | 26 VALIDATION_STRINGENCY="${validation_stringency}" |
| 27 QUIET=true | |
| 28 VERBOSITY=ERROR | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
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29 @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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30 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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31 ]]></command> |
| 5 | 32 <inputs> |
| 33 <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"/> | |
| 34 <conditional name="reference_source"> | |
| 35 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 36 <option value="cached">Local cache</option> | |
| 37 <option value="history">History</option> | |
| 38 </param> | |
| 39 <when value="cached"> | |
| 40 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 41 <options from_data_table="all_fasta"> | |
| 42 </options> | |
| 43 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 44 </param> | |
| 45 </when> | |
| 46 <when value="history"> | |
| 47 <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" /> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/> | |
| 51 <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/> | |
| 52 <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/> | |
| 53 | |
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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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54 |
| 5 | 55 <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
parents:
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56 |
| 5 | 57 </inputs> |
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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 <outputs> |
| 60 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
| 61 </outputs> | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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changeset
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62 |
| 5 | 63 <tests> |
| 64 <test> | |
| 65 <param name="reference_source_selector" value="history" /> | |
| 66 <param name="minimum_mapping_quality" value="20" /> | |
| 67 <param name="minimum_base_quality" value="20" /> | |
| 68 <param name="coverage_cap" value="250" /> | |
| 69 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> | |
| 70 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> | |
| 71 <output name="outFile" file="picard_CollectWgsMetrics_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
devteam
parents:
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72 </test> |
| 5 | 73 </tests> |
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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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74 |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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75 |
| 5 | 76 <help> |
| 77 | |
| 78 .. class:: infomark | |
| 79 | |
| 80 **Purpose** | |
| 81 | |
| 82 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 83 | |
| 84 @dataset_collections@ | |
| 85 | |
| 86 @description@ | |
| 87 | |
| 88 MINIMUM_MAPPING_QUALITY=Integer | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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89 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. |
| 5 | 90 |
| 91 MINIMUM_BASE_QUALITY=Integer | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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diff
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92 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. |
| 5 | 93 |
| 94 COVERAGE_CAP=Integer | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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diff
changeset
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95 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. |
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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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parents:
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96 Default value: 250. |
| 5 | 97 |
| 98 @more_info@ | |
| 99 | |
| 100 </help> | |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
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diff
changeset
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101 <expand macro="citations" /> |
| 5 | 102 </tool> |