Mercurial > repos > devteam > picard
annotate picard_CollectAlignmentSummaryMetrics.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 | 5eaa8a968300 |
| 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
devteam
parents:
5
diff
changeset
|
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>writes a file containing summary alignment metrics</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( $reference_source.ref_file.fields.path ) | |
| 17 #end if | |
| 18 | |
| 19 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 20 CollectAlignmentSummaryMetrics | |
| 21 INPUT="${inputFile}" | |
| 22 OUTPUT="${outFile}" | |
| 23 MAX_INSERT_SIZE=${maxinsert} | |
| 24 #for $sequence in $adapters: | |
| 25 ADAPTER_SEQUENCE="${sequence.adapter}" | |
| 26 #end for | |
| 27 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" | |
| 28 IS_BISULFITE_SEQUENCED="${bisulphite}" | |
| 29 | |
| 30 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 31 | |
| 32 ASSUME_SORTED="${assume_sorted}" | |
| 33 | |
| 34 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 35 QUIET=true | |
| 36 VERBOSITY=ERROR | |
| 37 | |
| 38 </command> | |
| 39 <inputs> | |
| 40 <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."/> | |
| 41 <conditional name="reference_source"> | |
| 42 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 43 <option value="cached">Local cache</option> | |
| 44 <option value="history">History</option> | |
| 45 </param> | |
| 46 <when value="cached"> | |
| 47 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 48 <options from_data_table="all_fasta"> | |
| 49 </options> | |
| 50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 51 </param> | |
| 52 </when> | |
| 53 <when value="history"> | |
|
8
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
54 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> |
| 5 | 55 </when> |
| 56 </conditional> | |
| 57 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
| 58 <option value="ALL_READS" selected="True">All reads</option> | |
| 59 <option value="SAMPLE">Sample</option> | |
| 60 <option value="LIBRARY">Library</option> | |
| 61 <option value="READ_GROUP">Read group</option> | |
| 62 </param> | |
| 63 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
| 64 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> | |
| 65 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> | |
| 66 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> | |
| 67 </repeat> | |
| 68 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/> | |
| 69 | |
| 70 <expand macro="VS" /> | |
| 71 | |
| 72 </inputs> | |
| 73 | |
| 74 <outputs> | |
| 75 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
| 76 </outputs> | |
| 77 | |
| 78 <stdio> | |
| 79 <exit_code range="1:" level="fatal"/> | |
| 80 </stdio> | |
| 81 | |
| 82 | |
| 83 <tests> | |
| 84 <test> | |
| 85 <param name="bisulphite" value="false" /> | |
| 86 <param name="sorted" value="true" /> | |
| 87 <param name="adaptors" value="" /> | |
| 88 <param name="maxinsert" value="100000" /> | |
| 89 <param name="reference_source_selector" value="history" /> | |
| 90 <param name="ref_file" value="picard_CASM_ref.fa" /> | |
| 91 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> | |
| 92 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 93 </test> | |
| 94 </tests> | |
| 95 | |
| 96 <help> | |
| 97 | |
| 98 .. class:: infomark | |
| 99 | |
| 100 **Purpose** | |
| 101 | |
| 102 Reads a SAM or BAM file and writes a file containing summary alignment metrics. | |
| 103 | |
| 104 @dataset_collections@ | |
| 105 | |
| 106 @description@ | |
| 107 | |
| 108 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with | |
| 109 inter-chromosomal pairs. Default value: 100000. | |
| 110 | |
| 111 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may | |
| 112 be specified 0 or more times. | |
| 113 | |
| 114 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
| 115 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
| 116 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
| 117 | |
| 118 IS_BISULFITE_SEQUENCED=Boolean | |
| 119 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. | |
| 120 | |
| 121 | |
| 122 REFERENCE_SEQUENCE=File | |
| 123 R=File Reference sequence fasta Default value: null. | |
| 124 | |
| 125 ASSUME_SORTED=Boolean | |
| 126 AS=Boolean If true (default), then the sort order in the header file will be ignored. | |
| 127 | |
| 128 @more_info@ | |
| 129 | |
| 130 </help> | |
| 131 </tool> | |
| 132 | |
| 133 |