Mercurial > repos > devteam > picard
annotate picard_CollectWgsMetrics.xml @ 13:7e6fd3d0f16e draft
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 |
| rev | line source |
|---|---|
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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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1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>compute metrics for evaluating of whole genome sequencing experiments</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </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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6 <expand macro="requirements" /> |
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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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7 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 8 @java_options@ |
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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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9 @symlink_element_identifier@ |
| 5 | 10 ##set up input files |
| 11 | |
| 12 #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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13 |
| 5 | 14 #if str( $reference_source.reference_source_selector ) == "history": |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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diff
changeset
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15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
| 5 | 16 #else: |
| 17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 18 #end if | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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19 |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
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20 picard |
| 5 | 21 CollectWgsMetrics |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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parents:
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diff
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22 INPUT='$inputFile.element_identifier' |
| 5 | 23 OUTPUT="${outFile}" |
| 24 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" | |
| 26 MINIMUM_BASE_QUALITY="${minimum_base_quality}" | |
| 27 COVERAGE_CAP="${coverage_cap}" | |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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28 |
| 5 | 29 VALIDATION_STRINGENCY="${validation_stringency}" |
| 30 QUIET=true | |
| 31 VERBOSITY=ERROR | |
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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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32 |
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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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changeset
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33 ]]></command> |
| 5 | 34 <inputs> |
| 35 <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"/> | |
| 36 <conditional name="reference_source"> | |
| 37 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 38 <option value="cached">Local cache</option> | |
| 39 <option value="history">History</option> | |
| 40 </param> | |
| 41 <when value="cached"> | |
| 42 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 43 <options from_data_table="all_fasta"> | |
| 44 </options> | |
| 45 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 46 </param> | |
| 47 </when> | |
| 48 <when value="history"> | |
| 49 <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" /> | |
| 50 </when> | |
| 51 </conditional> | |
| 52 <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"/> | |
| 53 <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"/> | |
| 54 <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"/> | |
| 55 | |
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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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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
parents:
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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
devteam
parents:
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60 |
| 5 | 61 <outputs> |
| 62 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
| 63 </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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diff
changeset
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64 |
| 5 | 65 <tests> |
| 66 <test> | |
| 67 <param name="reference_source_selector" value="history" /> | |
| 68 <param name="minimum_mapping_quality" value="20" /> | |
| 69 <param name="minimum_base_quality" value="20" /> | |
| 70 <param name="coverage_cap" value="250" /> | |
| 71 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> | |
| 72 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> | |
| 73 <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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74 </test> |
| 5 | 75 </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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76 |
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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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77 |
| 5 | 78 <help> |
| 79 | |
| 80 .. class:: infomark | |
| 81 | |
| 82 **Purpose** | |
| 83 | |
| 84 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 85 | |
| 86 @dataset_collections@ | |
| 87 | |
| 88 @description@ | |
| 89 | |
| 90 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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91 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. |
| 5 | 92 |
| 93 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
changeset
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94 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. |
| 5 | 95 |
| 96 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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97 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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98 Default value: 250. |
| 5 | 99 |
| 100 @more_info@ | |
| 101 | |
| 102 </help> | |
| 103 </tool> | |
| 104 | |
| 105 |