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annotate bam2wig.xml @ 5:09a89ed6f8fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 734a31ae8ba22f0d75bda696c4856ee3e274e1ba
author iuc
date Tue, 20 Mar 2018 05:37:00 -0400
parents 71ed55a3515a
children d7f6b3653d84
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1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@WRAPPER_VERSION@">
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2 <description>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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3 converts all types of RNA-seq data from .bam to .wig
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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4 </description>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[bam2wig.py --version]]></version_command>
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16 <command><![CDATA[
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17 ln -sf '${input}' 'input.bam' &&
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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18 ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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19 bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile
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21 #if str($strand_type.strand_specific) == "pair"
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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22 -d
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23 #if str($strand_type.pair_type) == "sd"
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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24 '1++,1--,2+-,2-+'
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25 #else
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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26 '1+-,1-+,2++,2--'
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27 #end if
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28 #end if
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29
3
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30 #if str($strand_type.strand_specific) == "single"
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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31 -d
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32 #if str($strand_type.single_type) == "s"
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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33 '++,--'
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 #else
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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35 '+-,-+'
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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36 #end if
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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37 #end if
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38
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39 #if str($wigsum_type.wigsum_type_selector) == "normalize":
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40 -t ${wigsum_type.totalwig}
3
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41 #end if
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42
3
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43 @MULTIHITS@
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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44 ]]>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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45 </command>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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46 <inputs>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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47 <expand macro="bam_param" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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48 <param name="chromsize" type="data" label="Chromosome size file (tab or space separated)" format="txt,tabular" help="(--chromSize)"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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49 <expand macro="multihits_param" />
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50 <conditional name="wigsum_type">
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51 <param name="wigsum_type_selector" type="select" label="Normalization">
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52 <option value="normalize">Normalize to specified sum</option>
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53 <option value="raw" selected="true">Do not normalize</option>
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54 </param>
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55 <when value="normalize">
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56 <param name="totalwig" value="" type="integer" label="specified wigsum" help="(--wigsum)"/>
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57 </when>
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58 <when value="raw"/>
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59 </conditional>
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60 <expand macro="strand_type_param" />
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61 </inputs>
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62
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63 <outputs>
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64 <data format="wig" name="output" from_work_dir="outfile.wig">
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65 <filter>strand_type['strand_specific'] == 'none'</filter>
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66 </data>
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67 <data format="wig" name="outputfwd" from_work_dir="outfile.Forward.wig" label="${tool.name} on ${on_string} (Forward Reads)">
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68 <filter>strand_type['strand_specific'] != 'none'</filter>
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69 </data>
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70 <data format="wig" name="outputrv" from_work_dir="outfile.Reverse.wig" label="${tool.name} on ${on_string} (Reverse Reads)">
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71 <filter>strand_type['strand_specific'] != 'none'</filter>
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72 </data>
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73 </outputs>
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74
3
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75 <tests>
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76 <test>
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77 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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78 <param name="chromsize" value="hg19.chrom.sizes"/>
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79 <output name="output" file="testwig.wig"/>
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80 </test>
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81 <test>
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82 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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83 <param name="chromsize" value="hg19.chrom.sizes"/>
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84 <param name="multihits_type_selector" value="skip_multihits"/>
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85 <param name="mapq" value="20"/>
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86 <output name="output" file="testwig.wig"/>
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87 </test>
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88 <test>
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89 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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90 <param name="chromsize" value="hg19.chrom.sizes"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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91 <param name="strand_specific" value="pair"/>
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92 <param name="pair_type" value="sd"/>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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93 <output name="outputfwd" file="testwig.Forward.wig"/>
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94 <output name="outputrv" file="testwig.Reverse.wig"/>
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95 </test>
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96 <test>
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97 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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98 <param name="chromsize" value="hg19.chrom.sizes"/>
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99 <param name="wigsum_type_selector" value="normalize"/>
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100 <param name="totalwig" value="100"/>
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101 <output name="output" file="testwig_wigsum100.wig"/>
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102 </test>
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103 </tests>
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104
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105 <help><![CDATA[
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106 bam2wig.py
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107 ++++++++++
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108
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109 Visualization is the most straightforward and effective way to QC your RNA-seq
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110 data. For example, change of expression or new splicing can be easily checked
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111 by visually comparing two RNA-seq tracks using genome browser such as UCSC_,
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112 IGB_ and IGV_. `bam2wig.py` converts all types of RNA-seq data from BAM_
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113 format into wiggle_ format in one-stop. wiggle_ files can then be easily
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114 converted into bigwig_. Bigwig is indexed, binary format of wiggle file, and
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115 it's particular useful to display large, continuous dataset on genome
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116 browser.
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117
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118 Inputs
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119 ++++++++++++++
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120
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121 Input BAM file
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122 Alignment file in BAM format (SAM is not supported). BAM file will be sorted and indexed using samTools.
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123
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124 Chromosome size file
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125 Tab or space separated text file with 2 columns: first column is chromosome name, second column is size of the chromosome. Chromosome names (such as "chr1") should be consistent between this file and BAM file.
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126
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127 Specified wigsum (default=none)
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128 Specified wigsum. Wigsum of 100000000 equals to coverage achieved by 1 million 100nt reads. Ignore this option to disable normalization.
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129
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130 Skip multiple Hit reads
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131 skips multiple hit reads or only use uniquely mapped reads
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132
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133 Strand-specific (default=none)
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134 How read(s) were stranded during sequencing. If you are not sure about the strand rule, run infer_experiment.py
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135
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136 Outputs
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137 ++++++++++++++
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138
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139 If RNA-seq is not strand specific, one wig file will be generated, if RNA-seq
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140 is strand specific, two wig files corresponding to Forward and Reverse will be generated.
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141
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142 @ABOUT@
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143
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144 .. _UCSC: http://genome.ucsc.edu/index.html
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145 .. _IGB: http://bioviz.org/igb/
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146 .. _IGV: http://software.broadinstitute.org/software/igv/
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147 .. _BAM: http://genome.ucsc.edu/goldenPath/help/bam.html
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148 .. _wiggle: http://genome.ucsc.edu/goldenPath/help/wiggle.html
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149 .. _bigwig: http://genome.ucsc.edu/FAQ/FAQformat.html#format6.1
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150 ]]>
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151 </help>
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152
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153 <expand macro="citations" />
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154
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155 </tool>