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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.126.0">
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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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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11
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12 <command>
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13
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14 ## Set up input files
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15
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16 ## Reference sequences
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17
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18 #set $reference_fasta_filename = "localref.fa"
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19
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20 #if str( $reference_source.reference_source_selector ) == "history":
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21 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
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22 #else:
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23 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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24 #end if
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25
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26 ## refFlat data
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27 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
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28
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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 &&
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30
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31 ## Start picard command
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32
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33 @java_options@
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34 java -jar \$JAVA_JAR_PATH/picard.jar
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35 CollectRnaSeqMetrics
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36 REF_FLAT=refFlat.tab
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37
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38 #if str( $ribosomal_intervals ) != "None":
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39 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
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40 #end if
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41
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42 STRAND_SPECIFICITY="${strand_specificity}"
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43 MINIMUM_LENGTH="${minimum_length}"
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44 CHART_OUTPUT="${pdfFile}"
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45
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46 #for $sequence_to_ignore in $ignore_list:
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47 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
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48 #end for
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49
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50 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
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51 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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52 INPUT="${inputFile}"
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53 OUTPUT="${outFile}"
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54 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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55 ASSUME_SORTED="${assume_sorted}"
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56
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57 QUIET=true
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58 VERBOSITY=ERROR
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59 VALIDATION_STRINGENCY=${validation_stringency}
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60
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61 </command>
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62
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63 <inputs>
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64 <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" />
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65 <conditional name="reference_source">
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66 <param name="reference_source_selector" type="select" label="Load reference genome from">
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67 <option value="cached">Local cache</option>
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68 <option value="history">History</option>
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69 </param>
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70 <when value="cached">
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71 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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72 <options from_data_table="all_fasta"></options>
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73 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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74 </param>
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75 </when>
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76 <when value="history">
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77 <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" />
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78 </when>
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79 </conditional>
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80 <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help" />
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81 <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"/>
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82 <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.">
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83 <option value="NONE" select="True">None</option>
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84 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
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85 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
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86 </param>
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87 <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"/>
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88 <repeat name="ignore_list" title="Sequences to ignore" min="0" help="You can provide multiple sequences by clicking the button below">
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89 <param name="sequence" type="text" size="80" label="Ignore reads matching this sequence"/>
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90 </repeat>
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91 <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"/>
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92 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
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93 <option value="ALL_READS" selected="True">All reads</option>
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94 <option value="SAMPLE">Sample</option>
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95 <option value="LIBRARY">Library</option>
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96 <option value="READ_GROUP">Read group</option>
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97 </param>
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98 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
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99
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100 <expand macro="VS" />
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101
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102 </inputs>
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103 <outputs>
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104 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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105 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
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106 </outputs>
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107
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108 <stdio>
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109 <exit_code range="1:" level="fatal"/>
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110 </stdio>
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111 <tests>
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112 <test>
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113 <param name="reference_source_selector" value="history"/>
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114 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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115 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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116 <param name="assume_sorted" value="true" />
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117 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
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118 <param name="metric_accumulation_level" value="ALL_READS" />
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119 <param name="minimum_length" value="500" />
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120 <param name="strand_specificity" value="NONE" />
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121 <param name="rrna_fragment_percentage" value="0.8" />
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122 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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123 </test>
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124
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125 </tests>
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126 <help>
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127
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128 .. class:: infomark
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129
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130 **Purpose**
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131
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132 Collects metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal.
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133
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134 @dataset_collections@
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135
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136 -----
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137
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138 .. class:: warningmark
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139
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140 **Obtaining gene annotations in refFlat format**
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141
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142 This tool requires gene annotations in refFlat_ format. These data can be obtained from UCSC table browser directly through Galaxy by following these steps:
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143
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144 1. Click on **Get Data** in the upper part of left pane of Galaxy interface
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145 2. Click on **UCSC Main** link
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146 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
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147 4. In the **output format** field choose **selected fields from primary and related tables**
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148 5. Click **get output** button
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149 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields:
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150 name
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151 chrom
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152 strand
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153 txStart
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154 txEnd
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155 cdsStart
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156 cdsEnd
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157 exonCount
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158 exonStarts
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159 exonEnds
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160 proteinId
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161 7. Click **done with selection**
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162 8. Click **Send query to Galaxy**
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163 9. A new dataset will appear in the current Galaxy history
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164 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
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165
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166 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat
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167
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168 @description@
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169
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170 REF_FLAT=File Gene annotations in refFlat form. Format described here:
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171 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
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172
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173 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases
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174 will be identified as being ribosomal. Format described here:
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175 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be
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176 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
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177
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178 STRAND_SPECIFICITY=StrandSpecificity
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179 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
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180 if the reads are expected to be on the transcription strand. Required. Possible values:
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181 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
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182
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183 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this
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184 length or greater. Default value: 500.
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185
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186 IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are
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187 counted as ignored bases.
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188
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189 RRNA_FRAGMENT_PERCENTAGE=Double
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190 This percentage of the length of a fragment must overlap one of the ribosomal intervals
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191 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8.
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192
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193 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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194 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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195 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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196
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197 ASSUME_SORTED=Boolean
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198 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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199 value: true. Possible values: {true, false}
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200
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201 @more_info@
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202
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203 </help>
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204 </tool>
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