Mercurial > repos > devteam > picard
annotate picard_CollectWgsMetrics.xml @ 32:f9242e01365a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
| author | iuc |
|---|---|
| date | Mon, 25 Sep 2023 08:32:17 +0000 |
| parents | 2a17c789e0a5 |
| children | 3f254c5ced1d |
| 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="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> | |
|
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 | 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" /> |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
8 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 9 @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
|
10 @symlink_element_identifier@ |
| 5 | 11 ##set up input files |
| 12 | |
| 13 #set $reference_fasta_filename = "localref.fa" | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
14 |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
14
diff
changeset
|
15 @handle_reference_source@ |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
16 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
17 picard |
| 5 | 18 CollectWgsMetrics |
|
14
465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents:
13
diff
changeset
|
19 INPUT='$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="${coverage_cap}" | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
25 |
| 5 | 26 VALIDATION_STRINGENCY="${validation_stringency}" |
| 27 QUIET=true | |
| 28 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
|
29 |
|
12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
8
diff
changeset
|
30 ]]></command> |
| 5 | 31 <inputs> |
| 32 <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"/> | |
| 33 <conditional name="reference_source"> | |
| 34 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 35 <option value="cached">Local cache</option> | |
| 36 <option value="history">History</option> | |
| 37 </param> | |
| 38 <when value="cached"> | |
| 39 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 40 <options from_data_table="all_fasta"> | |
| 41 </options> | |
| 42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 43 </param> | |
| 44 </when> | |
| 45 <when value="history"> | |
| 46 <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" /> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 <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"/> | |
| 50 <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"/> | |
| 51 <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"/> | |
| 52 | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
53 |
| 5 | 54 <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
|
55 |
| 5 | 56 </inputs> |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
57 |
| 5 | 58 <outputs> |
| 59 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
| 60 </outputs> | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
61 |
| 5 | 62 <tests> |
| 63 <test> | |
| 64 <param name="reference_source_selector" value="history" /> | |
| 65 <param name="minimum_mapping_quality" value="20" /> | |
| 66 <param name="minimum_base_quality" value="20" /> | |
| 67 <param name="coverage_cap" value="250" /> | |
| 68 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> | |
| 69 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> | |
| 70 <output name="outFile" file="picard_CollectWgsMetrics_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
|
71 </test> |
| 5 | 72 </tests> |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
73 |
|
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
74 |
| 5 | 75 <help> |
| 76 | |
| 77 .. class:: infomark | |
| 78 | |
| 79 **Purpose** | |
| 80 | |
| 81 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 82 | |
| 83 @dataset_collections@ | |
| 84 | |
| 85 @description@ | |
| 86 | |
| 87 MINIMUM_MAPPING_QUALITY=Integer | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
88 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. |
| 5 | 89 |
| 90 MINIMUM_BASE_QUALITY=Integer | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
91 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. |
| 5 | 92 |
| 93 COVERAGE_CAP=Integer | |
|
13
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
94 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. |
|
7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
12
diff
changeset
|
95 Default value: 250. |
| 5 | 96 |
| 97 @more_info@ | |
| 98 | |
| 99 </help> | |
|
19
5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
14
diff
changeset
|
100 <expand macro="citations" /> |
| 5 | 101 </tool> |