Mercurial > repos > devteam > picard
annotate picard_CollectGcBiasMetrics.xml @ 9:5eaa8a968300 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 17:43:13 -0400 |
| parents | 3a3234d7a2e8 |
| children | 05087b27692a |
| 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
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changeset
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1 <tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>charts the GC bias 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
devteam
parents:
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changeset
|
6 <expand macro="requirements"> |
|
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
7 <requirement type="package" version="3.1.2">R</requirement> |
|
3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
5
diff
changeset
|
8 </expand> |
| 5 | 9 <command> |
| 10 @java_options@ | |
| 11 ##set up input files | |
| 12 | |
| 13 #set $reference_fasta_filename = "localref.fa" | |
| 14 | |
| 15 #if str( $reference_source.reference_source_selector ) == "history": | |
| 16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 17 #else: | |
| 18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 19 #end if | |
| 20 | |
| 21 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 22 CollectGcBiasMetrics | |
| 23 INPUT="${inputFile}" | |
| 24 OUTPUT="${outFile}" | |
| 25 CHART_OUTPUT="${pdfFile}" | |
| 26 SUMMARY_OUTPUT="${summaryFile}" | |
| 27 WINDOW_SIZE="${window_size}" | |
| 28 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" | |
| 29 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" | |
| 30 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 31 ASSUME_SORTED="${assume_sorted}" | |
| 32 | |
| 33 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 34 QUIET=true | |
| 35 VERBOSITY=ERROR | |
| 36 | |
| 37 </command> | |
| 38 <inputs> | |
| 39 <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."/> | |
| 40 <conditional name="reference_source"> | |
| 41 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 42 <option value="cached">Local cache</option> | |
| 43 <option value="history">History</option> | |
| 44 </param> | |
| 45 <when value="cached"> | |
| 46 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 47 <options from_data_table="all_fasta"> | |
| 48 </options> | |
| 49 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 50 </param> | |
| 51 </when> | |
| 52 <when value="history"> | |
| 53 <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" /> | |
| 54 </when> | |
| 55 </conditional> | |
| 56 <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/> | |
| 57 <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/> | |
| 58 <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> | |
| 59 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
| 60 | |
| 61 <expand macro="VS" /> | |
| 62 | |
| 63 </inputs> | |
| 64 | |
| 65 <outputs> | |
| 66 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
| 67 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> | |
| 68 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> | |
| 69 </outputs> | |
| 70 | |
| 71 <tests> | |
| 72 <test> | |
| 73 <param name="window_size" value="100" /> | |
| 74 <param name="minimum_genome_fraction" value="0.00005" /> | |
| 75 <param name="assume_sorted" value="true" /> | |
| 76 <param name="is_bisulfite_sequenced" value="true" /> | |
| 77 <param name="reference_source_selector" value="history" /> | |
| 78 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" /> | |
| 79 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" /> | |
| 80 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 81 </test> | |
| 82 </tests> | |
| 83 | |
| 84 <stdio> | |
| 85 <exit_code range="1:" level="fatal"/> | |
| 86 </stdio> | |
| 87 | |
| 88 <help> | |
| 89 | |
| 90 .. class:: infomark | |
| 91 | |
| 92 **Purpose** | |
| 93 | |
| 94 Program to chart the nucleotide distribution per cycle in a SAM or BAM file. | |
| 95 | |
| 96 @dataset_collections@ | |
| 97 | |
| 98 @description@ | |
| 99 | |
| 100 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: | |
| 101 false. Possible values: {true, false} | |
| 102 | |
| 103 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. | |
| 104 This option can be set to 'null' to clear the default value. Possible values: {true, | |
| 105 false} | |
| 106 | |
| 107 ASSUME_SORTED=Boolean | |
| 108 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True | |
| 109 | |
| 110 @more_info@ | |
| 111 | |
| 112 </help> | |
| 113 </tool> | |
| 114 | |
| 115 |