Mercurial > repos > nilesh > rseqc

annotate geneBody_coverage.xml @ 52:34e4c586e3c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
author iuc
date Tue, 21 Nov 2017 14:55:32 -0500
parents 09846d5169fa
children 5873cd7afb67
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34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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1 <tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" version="@WRAPPER_VERSION@.1">
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2 <description>
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3 Read coverage over gene body.
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
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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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9
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[geneBody_coverage.py --version]]></version_command>
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16 <command><![CDATA[
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17 #if str($batch_mode.batch_mode_selector) == "merge":
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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18 #import re
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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19 #set $input_list = []
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20 #for $i, $input in enumerate($batch_mode.inputs):
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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21 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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22 #if $safename in $input_list:
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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23 #set $safename = str($safename) + "." + str($i)
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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24 #end if
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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25 $input_list.append($safename)
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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26 ln -sf '${input}' '${safename}.bam' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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27 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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28 echo '${safename}.bam' >> 'input_list.txt' &&
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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29 #end for
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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30 geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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31 #else
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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32 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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33 ln -sf '${input}' '${safename}.bam' &&
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
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35 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output
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36 #end if
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37 ]]>
f242ee103277 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 91ad241aa3f34b70649d13a5f18611da7577a5ee
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38 </command>
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39
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40 <inputs>
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41 <conditional name="batch_mode">
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42 <param name="batch_mode_selector" type="select" label="Run each sample separately, or combine mutiple samples into one plot">
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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43 <option value="batch" selected="true">Run each sample separately</option>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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44 <option value="merge">Combine multiple samples into a single plot</option>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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45 </param>
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46 <when value="batch">
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47 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
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48 </when>
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49 <when value="merge">
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50 <param name="inputs" type="data" label="Input .bam file(s)" format="bam" help="(--input-file)" multiple="true"/>
34e4c586e3c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
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51 </when>
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52 </conditional>
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53 <expand macro="refgene_param" />
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54 <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length (default: 100)" help="Minimum mRNA length in bp, mRNA that are shorter than this value will be skipped (--minimum_length)." />
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55 <expand macro="rscript_output_param" />
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56 </inputs>
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57
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58 <outputs>
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59 <data name="outputcurvespdf" format="pdf" from_work_dir="output.geneBodyCoverage.curves.pdf" label="${tool.name} on ${on_string} (Curves pdf)" />
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60 <data name="outputheatmappdf" format="pdf" from_work_dir="output.geneBodyCoverage.heatMap.pdf" label="${tool.name} on ${on_string} (HeatMap pdf)">
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61 <filter>batch_mode['batch_mode_selector'] == 'merge' and len(inputs) >= 3</filter>
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62 </data>
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63 <expand macro="rscript_output_data" filename="output.geneBodyCoverage.r" />
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64 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (text)" />
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65 </outputs>
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66
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67 <!-- PDF Files contain R version, must avoid checking for diff -->
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68 <tests>
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69 <test>
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70 <conditional name="batch_mode">
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71 <param name="batch_mode_selector" value="batch" />
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72 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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73 </conditional>
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74 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
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75 <param name="rscript_output" value="true" />
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76 <output name="outputcurvespdf" file="output.geneBodyCoverage.curves.pdf" compare="sim_size" />
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77 <output name="outputr" file="output.geneBodyCoverage.r" />
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78 <output name="outputtxt" file="output.geneBodyCoverage.txt" />
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79 </test>
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80 <test>
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81 <conditional name="batch_mode">
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82 <param name="batch_mode_selector" value="merge" />
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83 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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84 </conditional>
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85 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" />
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86 <param name="rscript_output" value="true" />
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87 <output name="outputcurvespdf" file="output2.geneBodyCoverage.curves.pdf" compare="sim_size" />
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88 <output name="outputheatmappdf" file="output2.geneBodyCoverage.heatMap.pdf" compare="sim_size" />
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89 <output name="outputr" file="output2.geneBodyCoverage.r" />
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90 <output name="outputtxt" file="output2.geneBodyCoverage.txt" />
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91 </test>
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92
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93 </tests>
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94
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95 <help><![CDATA[
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96 ## geneBody_coverage.py
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97
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98 Read coverage over gene body. This module is used to check if read coverage is uniform and if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates plots illustrating the coverage profile along the gene body.
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99
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100 If 3 or more BAM files were provided. This program generates a lineGraph and a heatmap. If fewer than 3 BAM files were provided, only lineGraph is generated. See below for examples.
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101
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102 When heatmap is generated, samples are ranked by the "skewness" of the coverage: Sample with best (worst) coverage will be displayed at the top (bottom) of the heatmap.
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103 Coverage skewness was measured by `Pearson’s skewness coefficients <http://en.wikipedia.org/wiki/Skewness#Pearson.27s_skewness_coefficients>`_
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104
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105 .. image:: $PATH_TO_IMAGES/geneBody_workflow.png
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106 :width: 800 px
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107 :scale: 80 %
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108
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109
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110 ## Inputs
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111
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112 Input BAM/SAM file
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113 Alignment file in BAM/SAM format.
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114
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115 Reference gene model
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116 Gene Model in BED format.
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117
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118 Minimum mRNA length
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119 Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100).
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120
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121 ## Outputs
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122
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123 Text
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124 Table that includes the data used to generate the plots
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125
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126 R Script
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127 R script file that reads the data and generates the plot
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128
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129 PDF
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130 The final plot, in PDF format
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131
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132 Example plots:
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133 .. image:: $PATH_TO_IMAGES/Aug_26.geneBodyCoverage.curves.png
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134 :height: 600 px
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135 :width: 600 px
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136 :scale: 80 %
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137
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138 .. image:: $PATH_TO_IMAGES/Aug_26.geneBodyCoverage.heatMap.png
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139 :height: 600 px
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140 :width: 600 px
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141 :scale: 80 %
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142
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143 @ABOUT@
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144
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145 ]]>
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146 </help>
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147
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148 <expand macro="citations" />
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149
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150 </tool>