Mercurial > repos > devteam > picard
annotate picard_CollectRnaSeqMetrics.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
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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.0"> |
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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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2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> |
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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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3 <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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4 <import>picard_macros.xml</import> |
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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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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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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <requirement type="package" version="3.1.2">R</requirement> |
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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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8 </expand> |
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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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9 <command> |
| 5 | 10 |
| 11 ## Set up input files | |
| 12 | |
| 13 ## Reference sequences | |
| 14 | |
| 15 #set $reference_fasta_filename = "localref.fa" | |
| 16 | |
| 17 #if str( $reference_source.reference_source_selector ) == "history": | |
| 18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 19 #else: | |
| 20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
| 21 #end if | |
| 22 | |
| 23 ## refFlat data | |
| 24 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format | |
| 25 | |
| 26 grep -v '^#' ${refFlat} | awk '{print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab && | |
| 27 | |
| 28 ## Start picard command | |
| 29 | |
| 30 @java_options@ | |
| 31 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 32 CollectRnaSeqMetrics | |
| 33 REF_FLAT=refFlat.tab | |
| 34 | |
| 35 #if str( $ribosomal_intervals ) != "None": | |
| 36 RIBOSOMAL_INTERVALS="${ribosomal_intervals}" | |
| 37 #end if | |
| 38 | |
| 39 STRAND_SPECIFICITY="${strand_specificity}" | |
| 40 MINIMUM_LENGTH="${minimum_length}" | |
| 41 CHART_OUTPUT="${pdfFile}" | |
| 42 | |
| 43 #for $sequence_to_ignore in $ignore_list: | |
| 44 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}" | |
| 45 #end for | |
| 46 | |
| 47 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}" | |
| 48 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" | |
| 49 INPUT="${inputFile}" | |
| 50 OUTPUT="${outFile}" | |
| 51 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
| 52 ASSUME_SORTED="${assume_sorted}" | |
| 53 | |
| 54 QUIET=true | |
| 55 VERBOSITY=ERROR | |
| 56 VALIDATION_STRINGENCY=${validation_stringency} | |
| 57 | |
| 58 </command> | |
| 59 | |
| 60 <inputs> | |
| 61 <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
| 62 <conditional name="reference_source"> | |
| 63 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
| 64 <option value="cached">Local cache</option> | |
| 65 <option value="history">History</option> | |
| 66 </param> | |
| 67 <when value="cached"> | |
| 68 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
| 69 <options from_data_table="all_fasta"></options> | |
| 70 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 71 </param> | |
| 72 </when> | |
| 73 <when value="history"> | |
| 74 <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" /> | |
| 75 </when> | |
| 76 </conditional> | |
| 77 <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help" /> | |
| 78 <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/> | |
| 79 <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand."> | |
| 80 <option value="NONE" select="True">None</option> | |
| 81 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> | |
| 82 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> | |
| 83 </param> | |
| 84 <param name="minimum_length" type="integer" value="500" label="When calculating coverage based values use only use transcripts of this length or greater" help="MINIMUM_LENGTH; default=500"/> | |
| 85 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> | |
| 86 <param name="sequence" type="text" size="80" label="Ignore reads matching this sequence"/> | |
| 87 </repeat> | |
| 88 <param name="rrna_fragment_percentage" type="float" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair to be considered rRNA." help="RRNA_FRAGMENT_PERCENTAGE; default=0.8"/> | |
| 89 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
| 90 <option value="ALL_READS" selected="True">All reads</option> | |
| 91 <option value="SAMPLE">Sample</option> | |
| 92 <option value="LIBRARY">Library</option> | |
| 93 <option value="READ_GROUP">Read group</option> | |
| 94 </param> | |
| 95 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
| 96 | |
| 97 <expand macro="VS" /> | |
| 98 | |
| 99 </inputs> | |
| 100 <outputs> | |
| 101 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> | |
| 102 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
| 103 </outputs> | |
| 104 | |
| 105 <stdio> | |
| 106 <exit_code range="1:" level="fatal"/> | |
| 107 </stdio> | |
| 108 <tests> | |
| 109 <test> | |
| 110 <param name="reference_source_selector" value="history"/> | |
| 111 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> | |
| 112 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> | |
| 113 <param name="assume_sorted" value="true" /> | |
| 114 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> | |
| 115 <param name="metric_accumulation_level" value="ALL_READS" /> | |
| 116 <param name="minimum_length" value="500" /> | |
| 117 <param name="strand_specificity" value="NONE" /> | |
| 118 <param name="rrna_fragment_percentage" value="0.8" /> | |
| 119 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> | |
| 120 </test> | |
| 121 | |
| 122 </tests> | |
| 123 <help> | |
| 124 | |
| 125 .. class:: infomark | |
| 126 | |
| 127 **Purpose** | |
| 128 | |
| 129 Collects metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal. | |
| 130 | |
| 131 @dataset_collections@ | |
| 132 | |
| 133 ----- | |
| 134 | |
| 135 .. class:: warningmark | |
| 136 | |
| 137 **Obtaining gene annotations in refFlat format** | |
| 138 | |
| 139 This tool requires gene annotations in refFlat_ format. These data can be obtained from UCSC table browser directly through Galaxy by following these steps: | |
| 140 | |
| 141 1. Click on **Get Data** in the upper part of left pane of Galaxy interface | |
| 142 2. Click on **UCSC Main** link | |
| 143 3. Set your genome and dataset of interest. It **must** be the same genome build against which you have mapped the reads contained in the BAM file you are analyzing | |
| 144 4. In the **output format** field choose **selected fields from primary and related tables** | |
| 145 5. Click **get output** button | |
| 146 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields: | |
| 147 name | |
| 148 chrom | |
| 149 strand | |
| 150 txStart | |
| 151 txEnd | |
| 152 cdsStart | |
| 153 cdsEnd | |
| 154 exonCount | |
| 155 exonStarts | |
| 156 exonEnds | |
| 157 proteinId | |
| 158 7. Click **done with selection** | |
| 159 8. Click **Send query to Galaxy** | |
| 160 9. A new dataset will appear in the current Galaxy history | |
| 161 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool | |
| 162 | |
| 163 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat | |
| 164 | |
| 165 @description@ | |
| 166 | |
| 167 REF_FLAT=File Gene annotations in refFlat form. Format described here: | |
| 168 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. | |
| 169 | |
| 170 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases | |
| 171 will be identified as being ribosomal. Format described here: | |
| 172 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be | |
| 173 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool | |
| 174 | |
| 175 STRAND_SPECIFICITY=StrandSpecificity | |
| 176 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND | |
| 177 if the reads are expected to be on the transcription strand. Required. Possible values: | |
| 178 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} | |
| 179 | |
| 180 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this | |
| 181 length or greater. Default value: 500. | |
| 182 | |
| 183 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are | |
| 184 counted as ignored bases. | |
| 185 | |
| 186 RRNA_FRAGMENT_PERCENTAGE=Double | |
| 187 This percentage of the length of a fragment must overlap one of the ribosomal intervals | |
| 188 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. | |
| 189 | |
| 190 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
| 191 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
| 192 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
| 193 | |
| 194 ASSUME_SORTED=Boolean | |
| 195 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default | |
| 196 value: true. Possible values: {true, false} | |
| 197 | |
| 198 @more_info@ | |
| 199 | |
| 200 </help> | |
| 201 </tool> |