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comparison picard_CollectRnaSeqMetrics.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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12:05087b27692a 13:7e6fd3d0f16e
7 <requirement type="package" version="3.3.1">r</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 ## Set up input files 11 ## Set up input files
12 12 @symlink_element_identifier@
13 ## Reference sequences 13 ## Reference sequences
14 14
15 #set $reference_fasta_filename = "localref.fa" 15 #set $reference_fasta_filename = "localref.fa"
16 16
17 #if str( $reference_source.reference_source_selector ) == "history": 17 #if str( $reference_source.reference_source_selector ) == "history":
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
19 #else: 19 #else:
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
21 #end if 21 #end if
22 22
23 ## refFlat data 23 ## refFlat data
24 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format 24 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
25 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 && 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 27
28 ## Start picard command 28 ## Start picard command
29 29
30 @java_options@ 30 @java_options@
31 picard 31 picard
32 CollectRnaSeqMetrics 32 CollectRnaSeqMetrics
33 REF_FLAT=refFlat.tab 33 REF_FLAT=refFlat.tab
34 34
35 #if str( $ribosomal_intervals ) != "None": 35 #if str( $ribosomal_intervals ) != "None":
36 RIBOSOMAL_INTERVALS="${ribosomal_intervals}" 36 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
37 #end if 37 #end if
38 38
39 STRAND_SPECIFICITY="${strand_specificity}" 39 STRAND_SPECIFICITY="${strand_specificity}"
40 MINIMUM_LENGTH="${minimum_length}" 40 MINIMUM_LENGTH="${minimum_length}"
41 CHART_OUTPUT="${pdfFile}" 41 CHART_OUTPUT="${pdfFile}"
42 42
43 #for $sequence_to_ignore in $ignore_list: 43 #for $sequence_to_ignore in $ignore_list:
44 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}" 44 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
45 #end for 45 #end for
46 46
47 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}" 47 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
48 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" 48 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
49 INPUT="${inputFile}" 49 INPUT='$inputFile.element_identifier'
50 OUTPUT="${outFile}" 50 OUTPUT="${outFile}"
51 REFERENCE_SEQUENCE="${reference_fasta_filename}" 51 REFERENCE_SEQUENCE="${reference_fasta_filename}"
52 ASSUME_SORTED="${assume_sorted}" 52 ASSUME_SORTED="${assume_sorted}"
53 53
54 QUIET=true 54 QUIET=true
55 VERBOSITY=ERROR 55 VERBOSITY=ERROR
56 VALIDATION_STRINGENCY=${validation_stringency} 56 VALIDATION_STRINGENCY=${validation_stringency}
57 57
58 ]]></command> 58 ]]></command>
59 59
60 <inputs> 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" /> 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"> 62 <conditional name="reference_source">
63 <param name="reference_source_selector" type="select" label="Load reference genome from"> 63 <param name="reference_source_selector" type="select" label="Load reference genome from">
64 <option value="cached">Local cache</option> 64 <option value="cached">Local cache</option>
71 </param> 71 </param>
72 </when> 72 </when>
73 <when value="history"> 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" /> 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> 75 </when>
76 </conditional> 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" /> 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"/> 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."> 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" selected="True">None</option> 80 <option value="NONE" selected="True">None</option>
81 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option> 81 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
91 <option value="SAMPLE">Sample</option> 91 <option value="SAMPLE">Sample</option>
92 <option value="LIBRARY">Library</option> 92 <option value="LIBRARY">Library</option>
93 <option value="READ_GROUP">Read group</option> 93 <option value="READ_GROUP">Read group</option>
94 </param> 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"/> 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 96
97 <expand macro="VS" /> 97 <expand macro="VS" />
98 98
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 101 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
102 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> 102 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
103 </outputs> 103 </outputs>
104 104
105 <tests> 105 <tests>
106 <test> 106 <test>
107 <param name="reference_source_selector" value="history"/> 107 <param name="reference_source_selector" value="history"/>
108 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/> 108 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
109 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/> 109 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
154 proteinId 154 proteinId
155 7. Click **done with selection** 155 7. Click **done with selection**
156 8. Click **Send query to Galaxy** 156 8. Click **Send query to Galaxy**
157 9. A new dataset will appear in the current Galaxy history 157 9. A new dataset will appear in the current Galaxy history
158 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool 158 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
159 159
160 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat 160 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
161 161
162 @description@ 162 @description@
163 163
164 REF_FLAT=File Gene annotations in refFlat form. Format described here: 164 REF_FLAT=File Gene annotations in refFlat form. Format described here:
165 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. 165 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
166 166
167 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases 167 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases
168 will be identified as being ribosomal. Format described here: 168 will be identified as being ribosomal. Format described here:
169 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be 169 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be
170 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool 170 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
171 171
172 STRAND_SPECIFICITY=StrandSpecificity 172 STRAND_SPECIFICITY=StrandSpecificity
173 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND 173 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
174 if the reads are expected to be on the transcription strand. Required. Possible values: 174 if the reads are expected to be on the transcription strand. Required. Possible values:
175 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} 175 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
176 176
177 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this 177 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this
178 length or greater. Default value: 500. 178 length or greater. Default value: 500.
179 179
180 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are 180 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are
181 counted as ignored bases. 181 counted as ignored bases.
182 182
183 RRNA_FRAGMENT_PERCENTAGE=Double 183 RRNA_FRAGMENT_PERCENTAGE=Double
184 This percentage of the length of a fragment must overlap one of the ribosomal intervals 184 This percentage of the length of a fragment must overlap one of the ribosomal intervals
185 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. 185 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8.
186 186
187 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel 187 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
188 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, 188 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
189 LIBRARY, READ_GROUP} This option may be specified 0 or more times. 189 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
190 190
191 ASSUME_SORTED=Boolean 191 ASSUME_SORTED=Boolean
192 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default 192 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
193 value: true. Possible values: {true, false} 193 value: true. Possible values: {true, false}
194 194
195 @more_info@ 195 @more_info@
196 196
197 </help> 197 </help>
198 </tool> 198 </tool>