Mercurial > repos > avowinkel > picard

comparison picard_CollectRnaSeqMetrics.xml @ 0:5166ed57b1c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5166ed57b1c4
1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.135">
2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="3.1.2">R</requirement>
8 </expand>
9 <command>
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}" &amp;&amp;
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 &amp;&amp;
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 &quot;Obtaining gene annotations in refFlat format&quot; 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>