Mercurial > repos > devteam > picard
annotate picard_CollectBaseDistributionByCycle.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 |
|---|---|
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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
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1 <tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</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
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6 <expand macro="requirements"> |
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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
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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:
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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( $reference_source.ref_file.fields.path ) | |
| 19 #end if | |
| 20 | |
| 21 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 22 CollectBaseDistributionByCycle | |
| 23 INPUT="${inputFile}" | |
| 24 OUTPUT="${outFile}" | |
| 25 CHART_OUTPUT="${pdfFile}" | |
| 26 ALIGNED_READS_ONLY="${aligned_reads_only}" | |
| 27 PF_READS_ONLY="${pf_reads_only}" | |
| 28 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 29 ASSUME_SORTED="${assume_sorted}" | |
| 30 | |
| 31 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 32 QUIET=true | |
| 33 VERBOSITY=ERROR | |
| 34 | |
| 35 </command> | |
| 36 <inputs> | |
| 37 <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."/> | |
| 38 <conditional name="reference_source"> | |
| 39 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 40 <option value="cached">Local cache</option> | |
| 41 <option value="history">History</option> | |
| 42 </param> | |
| 43 <when value="cached"> | |
| 44 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 45 <options from_data_table="all_fasta"> | |
| 46 </options> | |
| 47 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 48 </param> | |
| 49 </when> | |
| 50 <when value="history"> | |
| 51 <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" /> | |
| 52 </when> | |
| 53 </conditional> | |
| 54 <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/> | |
| 55 <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> | |
| 56 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
| 57 | |
| 58 <expand macro="VS" /> | |
| 59 | |
| 60 </inputs> | |
| 61 | |
| 62 <outputs> | |
| 63 <data format="tabular" name="outFile"/> | |
| 64 <data format="pdf" name="pdfFile"/> | |
| 65 </outputs> | |
| 66 | |
| 67 <tests> | |
| 68 <test> | |
| 69 <param name="aligned_reads_only" value="true" /> | |
| 70 <param name="pf_reads_only" value="true" /> | |
| 71 <param name="assume_sorted" value="true" /> | |
| 72 <param name="reference_source_selector" value="history" /> | |
| 73 <param name="ref_file" value="picard_CollectBaseDistributionByCycle_ref.fa" /> | |
| 74 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" /> | |
| 75 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 76 </test> | |
| 77 </tests> | |
| 78 | |
| 79 <stdio> | |
| 80 <exit_code range="1:" level="fatal"/> | |
| 81 </stdio> | |
| 82 | |
| 83 <help> | |
| 84 | |
| 85 .. class:: infomark | |
| 86 | |
| 87 **Purpose** | |
| 88 | |
| 89 Program to chart the nucleotide distribution per cycle in a SAM or BAM file. | |
| 90 | |
| 91 @dataset_collections@ | |
| 92 | |
| 93 @description@ | |
| 94 | |
| 95 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: | |
| 96 false. This option can be set to 'null' to clear the default value. Possible values: | |
| 97 {true, false} | |
| 98 | |
| 99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. | |
| 100 This option can be set to 'null' to clear the default value. Possible values: {true, | |
| 101 false} | |
| 102 | |
| 103 REFERENCE_SEQUENCE=File | |
| 104 R=File Reference sequence fasta Default value: null. | |
| 105 | |
| 106 ASSUME_SORTED=Boolean | |
| 107 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default | |
| 108 | |
| 109 @more_info@ | |
| 110 | |
| 111 </help> | |
| 112 </tool> | |
| 113 | |
| 114 |