Mercurial > repos > devteam > picard
annotate picard_CollectWgsMetrics.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 3d4f1fa26f0e |
| children | 05087b27692a |
| 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="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> | |
|
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" /> |
| 5 | 7 <command> |
| 8 @java_options@ | |
| 9 ##set up input files | |
| 10 | |
| 11 #set $reference_fasta_filename = "localref.fa" | |
| 12 | |
| 13 #if str( $reference_source.reference_source_selector ) == "history": | |
| 14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 15 #else: | |
| 16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 17 #end if | |
| 18 | |
| 19 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 20 CollectWgsMetrics | |
| 21 INPUT="${inputFile}" | |
| 22 OUTPUT="${outFile}" | |
| 23 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" | |
| 25 MINIMUM_BASE_QUALITY="${minimum_base_quality}" | |
| 26 COVERAGE_CAP="${coverage_cap}" | |
| 27 | |
| 28 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 29 QUIET=true | |
| 30 VERBOSITY=ERROR | |
| 31 | |
| 32 </command> | |
| 33 <inputs> | |
| 34 <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"/> | |
| 35 <conditional name="reference_source"> | |
| 36 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 37 <option value="cached">Local cache</option> | |
| 38 <option value="history">History</option> | |
| 39 </param> | |
| 40 <when value="cached"> | |
| 41 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 42 <options from_data_table="all_fasta"> | |
| 43 </options> | |
| 44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 45 </param> | |
| 46 </when> | |
| 47 <when value="history"> | |
| 48 <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" /> | |
| 49 </when> | |
| 50 </conditional> | |
| 51 <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"/> | |
| 52 <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"/> | |
| 53 <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"/> | |
| 54 | |
| 55 | |
| 56 <expand macro="VS" /> | |
| 57 | |
| 58 </inputs> | |
| 59 | |
| 60 <outputs> | |
| 61 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
| 62 </outputs> | |
| 63 | |
| 64 <tests> | |
| 65 <test> | |
| 66 <param name="reference_source_selector" value="history" /> | |
| 67 <param name="minimum_mapping_quality" value="20" /> | |
| 68 <param name="minimum_base_quality" value="20" /> | |
| 69 <param name="coverage_cap" value="250" /> | |
| 70 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> | |
| 71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> | |
| 72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 73 </test> | |
| 74 </tests> | |
| 75 | |
| 76 <stdio> | |
| 77 <exit_code range="1:" level="fatal"/> | |
| 78 </stdio> | |
| 79 | |
| 80 <help> | |
| 81 | |
| 82 .. class:: infomark | |
| 83 | |
| 84 **Purpose** | |
| 85 | |
| 86 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. | |
| 87 | |
| 88 @dataset_collections@ | |
| 89 | |
| 90 @description@ | |
| 91 | |
| 92 MINIMUM_MAPPING_QUALITY=Integer | |
| 93 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. | |
| 94 | |
| 95 MINIMUM_BASE_QUALITY=Integer | |
| 96 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. | |
| 97 | |
| 98 COVERAGE_CAP=Integer | |
| 99 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. | |
| 100 Default value: 250. | |
| 101 | |
| 102 @more_info@ | |
| 103 | |
| 104 </help> | |
| 105 </tool> | |
| 106 | |
| 107 |