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annotate picard_CollectRnaSeqMetrics.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents a1f0b3f4b781
children 3f254c5ced1d
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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">2</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.4.1">r-base</requirement>
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9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement>
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10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
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11 </expand>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ## Set up input files
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14 @symlink_element_identifier@
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15 ## Reference sequences
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16
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17 #set $reference_fasta_filename = "localref.fa"
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18
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19 @handle_reference_source@
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20
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21 ## refFlat data
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22 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
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24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
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25 #if $gene_reference_source.refFlat.ext == 'gff3'
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26 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
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27 #else
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28 gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
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29 #end if
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30 grep -v '^#' refFlat.tab.raw | awk '{print $12"\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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31 #else
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32 grep -v '^#' ${refFlat} | awk '{if ($3 == "+" || $3 == "-") print $11"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10; else print}' > refFlat.tab &&
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33 #end if
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34
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35 ## Start picard command
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36
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37 @java_options@
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38 picard
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39 CollectRnaSeqMetrics
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40 REF_FLAT=refFlat.tab
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41
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42 #if str( $ribosomal_intervals ) != "None":
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43 RIBOSOMAL_INTERVALS="${ribosomal_intervals}"
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44 #end if
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45
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46 STRAND_SPECIFICITY="${strand_specificity}"
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47 MINIMUM_LENGTH="${minimum_length}"
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48 CHART_OUTPUT="${pdfFile}"
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49
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50 #for $sequence_to_ignore in $ignore_list:
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51 IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"
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52 #end for
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53
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54 RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
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55 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
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56 INPUT='$escaped_element_identifier'
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57 OUTPUT="${outFile}"
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58 REFERENCE_SEQUENCE="${reference_fasta_filename}"
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59 ASSUME_SORTED="${assume_sorted}"
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60 VALIDATION_STRINGENCY=${validation_stringency}
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61
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62 ]]></command>
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63
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64 <inputs>
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65 <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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66 <conditional name="reference_source">
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67 <param name="reference_source_selector" type="select" label="Load reference genome from">
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68 <option value="cached">Local cache</option>
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69 <option value="history">History</option>
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70 </param>
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71 <when value="cached">
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72 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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73 <options from_data_table="all_fasta"></options>
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74 <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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75 </param>
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76 </when>
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77 <when value="history">
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78 <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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79 </when>
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80 </conditional>
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82 <conditional name="gene_reference_source">
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83 <param name="gene_reference_source_selector" type="select" label="Load gene annotation from">
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84 <option value="gtf">GTF/GFF3</option>
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85 <option value="refflat">refFlat</option>
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86 </param>
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87 <when value="gtf">
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88 <param name="refFlat"
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89 format="gtf,gff3"
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90 type="data"
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91 label="Gene annotation (GTF/GFF3)"/>
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92 </when>
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93 <when value="refflat">
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94 <param name="refFlat"
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95 format="tabular"
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96 type="data"
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97 label="Gene annotations in refFlat form"
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98 help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help"/>
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99 </when>
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100 </conditional>
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102
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103 <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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104 <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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105 <option value="NONE" selected="True">None</option>
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106 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
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107 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
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108 </param>
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109 <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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110 <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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111 <param name="sequence" type="text" label="Ignore reads matching this sequence"/>
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112 </repeat>
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113 <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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114 <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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115 <option value="ALL_READS" selected="True">All reads</option>
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116 <option value="SAMPLE">Sample</option>
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117 <option value="LIBRARY">Library</option>
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118 <option value="READ_GROUP">Read group</option>
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119 </param>
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120 <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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121
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122 <expand macro="VS" />
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123
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124 </inputs>
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125 <outputs>
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126 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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127 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
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128 </outputs>
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129
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130 <tests>
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131 <test>
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132 <param name="reference_source_selector" value="history"/>
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133 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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134 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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135 <param name="assume_sorted" value="true" />
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136
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137 <param name="gene_reference_source_selector" value="refflat" />
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138 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat" />
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139 <param name="metric_accumulation_level" value="ALL_READS" />
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140 <param name="minimum_length" value="500" />
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141 <param name="strand_specificity" value="NONE" />
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142 <param name="rrna_fragment_percentage" value="0.8" />
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143 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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144 </test>
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145 <test>
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146 <param name="reference_source_selector" value="history"/>
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147 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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148 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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149 <param name="assume_sorted" value="true" />
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150
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151 <param name="gene_reference_source_selector" value="refflat" />
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152 <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output" />
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153 <param name="metric_accumulation_level" value="ALL_READS" />
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154 <param name="minimum_length" value="500" />
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155 <param name="strand_specificity" value="NONE" />
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156 <param name="rrna_fragment_percentage" value="0.8" />
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157 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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158 </test>
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159
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160 <test>
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161 <param name="reference_source_selector" value="history"/>
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162 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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163 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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164 <param name="assume_sorted" value="true" />
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165
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166 <param name="gene_reference_source_selector" value="gtf" />
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167 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf" />
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168 <param name="metric_accumulation_level" value="ALL_READS" />
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169 <param name="minimum_length" value="500" />
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170 <param name="strand_specificity" value="NONE" />
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171 <param name="rrna_fragment_percentage" value="0.8" />
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172 <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/>
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173 </test>
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174
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175 <test>
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176 <param name="reference_source_selector" value="history"/>
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177 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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178 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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179 <param name="assume_sorted" value="true" />
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180
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181 <param name="gene_reference_source_selector" value="gtf" />
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182 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3" />
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183 <param name="metric_accumulation_level" value="ALL_READS" />
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184 <param name="minimum_length" value="500" />
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185 <param name="strand_specificity" value="NONE" />
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186 <param name="rrna_fragment_percentage" value="0.8" />
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187 <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>
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188 </test>
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189 </tests>
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190 <help>
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191
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192 .. class:: infomark
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193
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194 **Purpose**
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195
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196 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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197
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198 @dataset_collections@
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199
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200 -----
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201
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202 .. class:: warningmark
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203
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204 **Obtaining gene annotations in refFlat format**
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205
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206 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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207
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208 1. Click on **Get Data** in the upper part of left pane of Galaxy interface
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209 2. Click on **UCSC Main** link
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210 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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211 4. In the **output format** field choose **selected fields from primary and related tables**
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212 5. Click **get output** button
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213 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields:
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214 name
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215 chrom
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216 strand
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217 txStart
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218 txEnd
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219 cdsStart
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220 cdsEnd
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221 exonCount
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222 exonStarts
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223 exonEnds
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224 proteinId
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225 7. Click **done with selection**
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226 8. Click **Send query to Galaxy**
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227 9. A new dataset will appear in the current Galaxy history
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228 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
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229
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230 .. _refFlat: https://genome.ucsc.edu/FAQ/FAQformat.html#format9
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231
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232 @description@
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233
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234 REF_FLAT=File Gene annotations in refFlat form. Format described here:
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235 https://genome.ucsc.edu/FAQ/FAQformat.html#format9 Required.
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236
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237 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases
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238 will be identified as being ribosomal. Format described here:
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239 https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html and can be
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240 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
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241
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242 STRAND_SPECIFICITY=StrandSpecificity
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243 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
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244 if the reads are expected to be on the transcription strand. Required. Possible values:
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245 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
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246
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247 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this
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248 length or greater. Default value: 500.
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249
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250 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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251 counted as ignored bases.
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252
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253 RRNA_FRAGMENT_PERCENTAGE=Double
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254 This percentage of the length of a fragment must overlap one of the ribosomal intervals
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255 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8.
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256
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257 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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258 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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259 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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260
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261 ASSUME_SORTED=Boolean
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262 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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263 value: true. Possible values: {true, false}
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264
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265 @more_info@
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266
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267 </help>
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268 <expand macro="citations" />
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269 </tool>