Mercurial > repos > devteam > picard
annotate picard_CollectAlignmentSummaryMetrics.xml @ 11:efc56ee1ade4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:23:17 -0500 |
| parents | 777ccdd1d6e4 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1"> |
| 5 | 2 <description>writes a file containing summary alignment metrics</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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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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7 <stdio> |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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8 <exit_code range="1:" level="fatal"/> |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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9 </stdio> |
| 5 | 10 <command> |
| 11 @java_options@ | |
| 12 ##set up input files | |
| 13 | |
| 14 #set $reference_fasta_filename = "localref.fa" | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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15 |
| 5 | 16 #if str( $reference_source.reference_source_selector ) == "history": |
| 17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 18 #else: | |
| 19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 20 #end if | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
9
diff
changeset
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21 |
| 5 | 22 java -jar \$JAVA_JAR_PATH/picard.jar |
| 23 CollectAlignmentSummaryMetrics | |
| 24 INPUT="${inputFile}" | |
| 25 OUTPUT="${outFile}" | |
| 26 MAX_INSERT_SIZE=${maxinsert} | |
| 27 #for $sequence in $adapters: | |
| 28 ADAPTER_SEQUENCE="${sequence.adapter}" | |
| 29 #end for | |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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30 #for $level in str($metric_accumulation_level).split(','): |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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31 METRIC_ACCUMULATION_LEVEL="${level}" |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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changeset
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32 #end for |
| 5 | 33 IS_BISULFITE_SEQUENCED="${bisulphite}" |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
9
diff
changeset
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34 |
| 5 | 35 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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10
777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
9
diff
changeset
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36 |
| 5 | 37 ASSUME_SORTED="${assume_sorted}" |
| 38 | |
| 39 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 40 QUIET=true | |
| 41 VERBOSITY=ERROR | |
| 42 | |
| 43 </command> | |
| 44 <inputs> | |
| 45 <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."/> | |
| 46 <conditional name="reference_source"> | |
| 47 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 48 <option value="cached">Local cache</option> | |
| 49 <option value="history">History</option> | |
| 50 </param> | |
| 51 <when value="cached"> | |
| 52 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 53 <options from_data_table="all_fasta"> | |
| 54 </options> | |
| 55 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 56 </param> | |
| 57 </when> | |
| 58 <when value="history"> | |
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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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parents:
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changeset
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59 <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 | 60 </when> |
| 61 </conditional> | |
| 62 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
| 63 <option value="ALL_READS" selected="True">All reads</option> | |
| 64 <option value="SAMPLE">Sample</option> | |
| 65 <option value="LIBRARY">Library</option> | |
| 66 <option value="READ_GROUP">Read group</option> | |
| 67 </param> | |
| 68 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
| 69 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> | |
| 70 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> | |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
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71 <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> |
| 5 | 72 </repeat> |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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diff
changeset
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73 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/> |
| 5 | 74 <expand macro="VS" /> |
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777ccdd1d6e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
9
diff
changeset
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75 |
| 5 | 76 </inputs> |
| 77 <outputs> | |
| 78 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
| 79 </outputs> | |
| 80 <tests> | |
| 81 <test> | |
| 82 <param name="bisulphite" value="false" /> | |
| 83 <param name="sorted" value="true" /> | |
| 84 <param name="adaptors" value="" /> | |
| 85 <param name="maxinsert" value="100000" /> | |
| 86 <param name="reference_source_selector" value="history" /> | |
| 87 <param name="ref_file" value="picard_CASM_ref.fa" /> | |
| 88 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> | |
| 89 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 90 </test> | |
| 91 </tests> | |
| 92 <help> | |
| 93 | |
| 94 .. class:: infomark | |
| 95 | |
| 96 **Purpose** | |
| 97 | |
| 98 Reads a SAM or BAM file and writes a file containing summary alignment metrics. | |
| 99 | |
| 100 @dataset_collections@ | |
| 101 | |
| 102 @description@ | |
| 103 | |
| 104 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with | |
| 105 inter-chromosomal pairs. Default value: 100000. | |
| 106 | |
| 107 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may | |
| 108 be specified 0 or more times. | |
| 109 | |
| 110 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
| 111 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
| 112 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
| 113 | |
| 114 IS_BISULFITE_SEQUENCED=Boolean | |
| 115 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. | |
| 116 | |
| 117 | |
| 118 REFERENCE_SEQUENCE=File | |
| 119 R=File Reference sequence fasta Default value: null. | |
| 120 | |
| 121 ASSUME_SORTED=Boolean | |
| 122 AS=Boolean If true (default), then the sort order in the header file will be ignored. | |
| 123 | |
| 124 @more_info@ | |
| 125 | |
| 126 </help> | |
| 127 </tool> | |
| 128 | |
| 129 |