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annotate picard_CollectRnaSeqMetrics.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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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@">0</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="447">ucsc-gff3togenepred</requirement>
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9 <requirement type="package" version="447">ucsc-gtftogenepred</requirement>
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10 </expand>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## Set up input files
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13 @symlink_element_identifier@
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14 ## Reference sequences
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16 #set $reference_fasta_filename = "localref.fa"
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18 @handle_reference_source@
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19
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20 ## refFlat data
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21 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
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23 #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
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24 #if $gene_reference_source.refFlat.ext == 'gff3'
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25 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
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26 #else
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27 gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
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28 #end if
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29 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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30 #else
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31 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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32 #end if
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33
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34 ## Start picard command
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35
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36 @java_options@
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37 picard CollectRnaSeqMetrics
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38 --REF_FLAT refFlat.tab
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39
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40 #if str( $ribosomal_intervals ) != "None":
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41 --RIBOSOMAL_INTERVALS '${ribosomal_intervals}'
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42 #end if
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43
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44 --STRAND_SPECIFICITY '${strand_specificity}'
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45 --MINIMUM_LENGTH '${minimum_length}'
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46 --CHART_OUTPUT '${pdfFile}'
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47
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48 #for $sequence_to_ignore in $ignore_list:
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49 --IGNORE_SEQUENCE '${sequence_to_ignore.sequence}'
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50 #end for
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51
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52 --RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}'
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53 --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}'
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54 --INPUT '$escaped_element_identifier'
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55 -OUTPUT '${outFile}'
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56 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
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57 --ASSUME_SORTED '${assume_sorted}'
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58 --VALIDATION_STRINGENCY ${validation_stringency}
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59
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60 ]]></command>
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61 <inputs>
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62 <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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63 <conditional name="reference_source">
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64 <param name="reference_source_selector" type="select" label="Load reference genome from">
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65 <option value="cached">Local cache</option>
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66 <option value="history">History</option>
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67 </param>
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68 <when value="cached">
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69 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
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70 <options from_data_table="all_fasta"/>
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71 <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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72 </param>
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73 </when>
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74 <when value="history">
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75 <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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76 </when>
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77 </conditional>
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78 <conditional name="gene_reference_source">
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79 <param name="gene_reference_source_selector" type="select" label="Load gene annotation from">
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80 <option value="gtf">GTF/GFF3</option>
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81 <option value="refflat">refFlat</option>
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82 </param>
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83 <when value="gtf">
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84 <param name="refFlat" format="gtf,gff3" type="data" label="Gene annotation (GTF/GFF3)"/>
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85 </when>
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86 <when value="refflat">
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87 <param name="refFlat" format="tabular" type="data" label="Gene annotations in refFlat form" help="See &quot;Obtaining gene annotations in refFlat format&quot; below for help"/>
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88 </when>
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89 </conditional>
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90 <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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91 <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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92 <option value="NONE" selected="True">None</option>
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93 <option value="FIRST_READ_TRANSCRIPTION_STRAND">First read transcription strand</option>
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94 <option value="SECOND_READ_TRANSCRIPTION_STRAND">Second read transcription strand</option>
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95 </param>
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96 <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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97 <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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98 <param name="sequence" type="text" label="Ignore reads matching this sequence"/>
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99 </repeat>
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100 <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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101 <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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102 <option value="ALL_READS" selected="True">All reads</option>
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103 <option value="SAMPLE">Sample</option>
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104 <option value="LIBRARY">Library</option>
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105 <option value="READ_GROUP">Read group</option>
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106 </param>
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107 <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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108 <expand macro="VS"/>
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109 </inputs>
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110 <outputs>
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111 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
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112 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
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113 </outputs>
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114 <tests>
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115 <test>
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116 <param name="reference_source_selector" value="history"/>
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117 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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118 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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119 <param name="assume_sorted" value="true"/>
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120 <param name="gene_reference_source_selector" value="refflat"/>
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121 <param name="refFlat" value="picard_CollectRnaSeqMetrics.refFlat"/>
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122 <param name="metric_accumulation_level" value="ALL_READS"/>
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123 <param name="minimum_length" value="500"/>
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124 <param name="strand_specificity" value="NONE"/>
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125 <param name="rrna_fragment_percentage" value="0.8"/>
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126 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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127 </test>
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128 <test>
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129 <param name="reference_source_selector" value="history"/>
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130 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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131 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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132 <param name="assume_sorted" value="true"/>
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133 <param name="gene_reference_source_selector" value="refflat"/>
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134 <param name="refFlat" value="picard_CollectRnaSeqMetrics.ucsc_output"/>
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135 <param name="metric_accumulation_level" value="ALL_READS"/>
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136 <param name="minimum_length" value="500"/>
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137 <param name="strand_specificity" value="NONE"/>
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138 <param name="rrna_fragment_percentage" value="0.8"/>
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139 <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
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140 </test>
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141 <test>
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142 <param name="reference_source_selector" value="history"/>
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143 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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144 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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145 <param name="assume_sorted" value="true"/>
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146 <param name="gene_reference_source_selector" value="gtf"/>
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147 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gtf" ftype="gtf"/>
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148 <param name="metric_accumulation_level" value="ALL_READS"/>
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149 <param name="minimum_length" value="500"/>
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150 <param name="strand_specificity" value="NONE"/>
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151 <param name="rrna_fragment_percentage" value="0.8"/>
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152 <output name="outFile" file="picard_CollectRnaSeqMetrics_test2.tab" ftype="tabular" lines_diff="4"/>
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153 </test>
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154 <test>
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155 <param name="reference_source_selector" value="history"/>
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156 <param name="ref_file" value="picard_CollectRnaSeqMetrics_ref.fa" ftype="fasta"/>
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157 <param name="inputFile" value="picard_CollectRnaSeqMetrics.bam" ftype="bam"/>
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158 <param name="assume_sorted" value="true"/>
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159 <param name="gene_reference_source_selector" value="gtf"/>
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160 <param name="refFlat" value="picard_CollectRnaSeqMetrics.gff3" ftype="gff3"/>
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161 <param name="metric_accumulation_level" value="ALL_READS"/>
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162 <param name="minimum_length" value="500"/>
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163 <param name="strand_specificity" value="NONE"/>
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164 <param name="rrna_fragment_percentage" value="0.8"/>
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165 <output name="outFile" file="picard_CollectRnaSeqMetrics_test3.tab" ftype="tabular" lines_diff="4"/>
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166 </test>
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167 </tests>
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168 <help>
5
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169
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170 .. class:: infomark
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171
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172 **Purpose**
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173
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174 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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175
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176 @dataset_collections@
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177
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178 -----
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179
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180 .. class:: warningmark
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181
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182 **Obtaining gene annotations in refFlat format**
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183
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184 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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185
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186 1. Click on **Get Data** in the upper part of left pane of Galaxy interface
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187 2. Click on **UCSC Main** link
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188 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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189 4. In the **output format** field choose **selected fields from primary and related tables**
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190 5. Click **get output** button
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191 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields:
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192 name
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193 chrom
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194 strand
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195 txStart
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196 txEnd
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197 cdsStart
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198 cdsEnd
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199 exonCount
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200 exonStarts
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201 exonEnds
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202 proteinId
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203 7. Click **done with selection**
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204 8. Click **Send query to Galaxy**
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205 9. A new dataset will appear in the current Galaxy history
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206 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool
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207
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208 .. _refFlat: https://genome.ucsc.edu/FAQ/FAQformat.html#format9
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209
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210 @description@
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211
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212 REF_FLAT=File Gene annotations in refFlat form. Format described here:
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213 https://genome.ucsc.edu/FAQ/FAQformat.html#format9 Required.
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214
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215 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases
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216 will be identified as being ribosomal. Format described here:
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217 https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html and can be
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218 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
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219
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220 STRAND_SPECIFICITY=StrandSpecificity
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221 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
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222 if the reads are expected to be on the transcription strand. Required. Possible values:
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223 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
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224
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225 MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this
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226 length or greater. Default value: 500.
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227
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228 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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229 counted as ignored bases.
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230
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231 RRNA_FRAGMENT_PERCENTAGE=Double
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232 This percentage of the length of a fragment must overlap one of the ribosomal intervals
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233 for a read or read pair by this must in order to be considered rRNA. Default value: 0.8.
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234
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235 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
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236 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
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237 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
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238
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239 ASSUME_SORTED=Boolean
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240 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
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241 value: true. Possible values: {true, false}
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242
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243 @more_info@
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244
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245 </help>
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246 <expand macro="citations"/>
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247 </tool>