Mercurial > repos > devteam > picard_plus
comparison picard_CollectRnaSeqMetrics.xml @ 0:4419e9980172 draft
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author | devteam |
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date | Thu, 23 Oct 2014 12:03:34 -0400 |
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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.122.0"> | |
2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.122.0">picard</requirement> | |
5 </requirements> | |
6 | |
7 <macros> | |
8 <import>picard_macros.xml</import> | |
9 </macros> | |
10 | |
11 | |
12 <command> | |
13 | |
14 ## Set up input files | |
15 | |
16 ## Reference sequences | |
17 | |
18 #set $reference_fasta_filename = "localref.fa" | |
19 | |
20 #if str( $reference_source.reference_source_selector ) == "history": | |
21 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && | |
22 #else: | |
23 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | |
24 #end if | |
25 | |
26 ## refFlat data | |
27 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format | |
28 | |
29 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 && | |
30 | |
31 ## Start picard command | |
32 | |
33 @java_options@ | |
34 java -jar \$JAVA_JAR_PATH/CollectRnaSeqMetrics.jar | |
35 REF_FLAT=refFlat.tab | |
36 | |
37 #if str( $ribosomal_intervals ) != "None": | |
38 RIBOSOMAL_INTERVALS="${ribosomal_intervals}" | |
39 #end if | |
40 | |
41 STRAND_SPECIFICITY="${strand_specificity}" | |
42 MINIMUM_LENGTH="${minimum_length}" | |
43 CHART_OUTPUT="${pdfFile}" | |
44 | |
45 #for $sequence_to_ignore in $ignore_list: | |
46 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}" | |
47 #end for | |
48 | |
49 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}" | |
50 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" | |
51 INPUT="${inputFile}" | |
52 OUTPUT="${outFile}" | |
53 REFERENCE_SEQUENCE="${reference_fasta_filename}" | |
54 ASSUME_SORTED="${assume_sorted}" | |
55 | |
56 QUIET=true | |
57 VERBOSITY=ERROR | |
58 VALIDATION_STRINGENCY=${validation_stringency} | |
59 | |
60 </command> | |
61 | |
62 <inputs> | |
63 <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" /> | |
64 <conditional name="reference_source"> | |
65 <param name="reference_source_selector" type="select" label="Load reference genome from"> | |
66 <option value="cached">Local cache</option> | |
67 <option value="history">History</option> | |
68 </param> | |
69 <when value="cached"> | |
70 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> | |
71 <options from_data_table="all_fasta"></options> | |
72 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
73 </param> | |
74 </when> | |
75 <when value="history"> | |
76 <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" /> | |
77 </when> | |
78 </conditional> | |
79 <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help" /> | |
80 <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"/> | |
81 <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."> | |
82 <option value="NONE" select="True">None</option> | |
83 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> | |
84 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option> | |
85 </param> | |
86 <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"/> | |
87 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below"> | |
88 <param name="sequence" type="text" size="80" label="Ignore reads matching this sequence"/> | |
89 </repeat> | |
90 <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"/> | |
91 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> | |
92 <option value="ALL_READS" selected="True">All reads</option> | |
93 <option value="SAMPLE">Sample</option> | |
94 <option value="LIBRARY">Library</option> | |
95 <option value="READ_GROUP">Read group</option> | |
96 </param> | |
97 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> | |
98 | |
99 <expand macro="VS" /> | |
100 | |
101 </inputs> | |
102 <outputs> | |
103 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> | |
104 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> | |
105 </outputs> | |
106 | |
107 <stdio> | |
108 <exit_code range="1:" level="fatal"/> | |
109 </stdio> | |
110 <tests> | |
111 <test> | |
112 <param name="reference_source_selector" value="history"/> | |
113 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> | |
114 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> | |
115 <param name="assume_sorted" value="true" /> | |
116 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" /> | |
117 <param name="metric_accumulation_level" value="ALL_READS" /> | |
118 <param name="minimum_length" value="500" /> | |
119 <param name="strand_specificity" value="NONE" /> | |
120 <param name="rrna_fragment_percentage" value="0.8" /> | |
121 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/> | |
122 </test> | |
123 | |
124 </tests> | |
125 <help> | |
126 | |
127 .. class:: infomark | |
128 | |
129 **Purpose** | |
130 | |
131 Collects metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal. | |
132 | |
133 @dataset_collections@ | |
134 | |
135 ----- | |
136 | |
137 .. class:: warningmark | |
138 | |
139 **Obtaining gene annotations in refFlat format** | |
140 | |
141 This tool requires gene annotations in refFlat_ format. These data can be obtained from UCSC table browser directly through Galaxy by following these steps: | |
142 | |
143 1. Click on **Get Data** in the upper part of left pane of Galaxy interface | |
144 2. Click on **UCSC Main** link | |
145 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 | |
146 4. In the **output format** field choose **selected fields from primary and related tables** | |
147 5. Click **get output** button | |
148 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields: | |
149 name | |
150 chrom | |
151 strand | |
152 txStart | |
153 txEnd | |
154 cdsStart | |
155 cdsEnd | |
156 exonCount | |
157 exonStarts | |
158 exonEnds | |
159 proteinId | |
160 7. Click **done with selection** | |
161 8. Click **Send query to Galaxy** | |
162 9. A new dataset will appear in the current Galaxy history | |
163 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool | |
164 | |
165 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat | |
166 | |
167 @description@ | |
168 | |
169 REF_FLAT=File Gene annotations in refFlat form. Format described here: | |
170 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. | |
171 | |
172 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases | |
173 will be identified as being ribosomal. Format described here: | |
174 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be | |
175 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool | |
176 | |
177 STRAND_SPECIFICITY=StrandSpecificity | |
178 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND | |
179 if the reads are expected to be on the transcription strand. Required. Possible values: | |
180 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} | |
181 | |
182 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this | |
183 length or greater. Default value: 500. | |
184 | |
185 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are | |
186 counted as ignored bases. | |
187 | |
188 RRNA_FRAGMENT_PERCENTAGE=Double | |
189 This percentage of the length of a fragment must overlap one of the ribosomal intervals | |
190 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. | |
191 | |
192 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel | |
193 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, | |
194 LIBRARY, READ_GROUP} This option may be specified 0 or more times. | |
195 | |
196 ASSUME_SORTED=Boolean | |
197 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default | |
198 value: true. Possible values: {true, false} | |
199 | |
200 @more_info@ | |
201 | |
202 </help> | |
203 </tool> |