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annotate sam_dump.xml @ 2:6aa2efbe5920 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author iuc
date Fri, 16 Sep 2016 17:23:44 -0400
parents 069a879beef7
children 62367c99119d
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2
6aa2efbe5920 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
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1 <tool id="sam_dump" name="Extract reads" version="2.6.2">
0
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2 <description>in SAM or BAM format from NCBI SRA.</description>
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3 <macros>
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4 <import>sra_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>sam-dump --version</version_command>
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8 <command>
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9 <![CDATA[
1
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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10 #if $input.input_select=="file_list":
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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11 for acc in `cat $input.file_list` ;
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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12 do
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13 #elif $input.input_select=="accession_number":
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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14 acc="$input.accession" &&
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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15 #end if
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17 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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19 #end if
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069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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069a879beef7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 8550e0c7389533bebc75d7a93b89a3e59fe77bcd
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22
0
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23 ## Need to set the home directory to the current working directory,
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6aa2efbe5920 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
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24 ## else the tool tries to write to home/.ncbi and fails when used
6aa2efbe5920 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
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25 ## with a cluster manager.
0
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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26 export HOME=\$PWD &&
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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27 vdb-config --restore-defaults &&
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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28 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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29 ## Do not use prefetch if region is specified, to avoid downloading
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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30 ## the complete sra file.
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31 #if ( str( $adv.region ) == "" ):
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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32 ASCP_PATH=`command -v ascp` &&
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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33 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
1
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34 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
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20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 ## Duplicate vdb-config, in case settings changed between prefetch and
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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36 ## dump command.
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37 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
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38 #end if
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39 sam-dump --log-level fatal --disable-multithreading
20da3b075bbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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40 #if str( $adv.region ) != "":
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41 --aligned-region "$adv.region"
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42 #end if
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43 #if str( $adv.matepairDist ) != "":
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44 --matepair-distance "$adv.matepairDist"
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45 #end if
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46 #if str( $adv.minMapq ) != "":
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47 --min-mapq "$adv.minMapq"
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48 #end if
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49 #if str( $adv.header ) == "yes":
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50 --header
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51 #else:
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52 --no-header
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53 #end if
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54 #if str( $adv.alignments ) == "both":
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55 --unaligned
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56 #end if
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57 #if str( $adv.alignments ) == "unaligned":
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58 --unaligned-spots-only
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59 #end if
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60 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
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61 --primary
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62 #end if
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63 #if $input.input_select == "file":
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64 "$input.file"
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65 #elif $input.input_select == "accession_number":
1
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66 "\$acc"
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67 #elif $input.input_select=="file_list":
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68 "\$acc"
0
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69 #end if
2
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70
0
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71 #if str( $outputformat ) == "bam":
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72 | samtools view -Sb - 2> /dev/null
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73 #end if
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74 #if $input.input_select == "file":
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75 > "$output_file"
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76 #elif $input.input_select == "accession_number":
1
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77 > "$output_accession" )
0
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78 #end if
1
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79
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80 #if $input.input_select=="file_list":
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81 #if str( $outputformat ) == "bam":
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82 > "\$acc.bam"
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83 #elif str( $outputformat ) == "sam":
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84 > "\$acc.sam"
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85 #end if
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86 ) ; done
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87 #end if
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88
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89
0
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90 ]]>
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91 </command>
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92 <inputs>
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93 <expand macro="input_conditional"/>
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94 <param name="outputformat" type="select" label="select output format">
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95 <option value="bam">bam</option>
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96 <option value="sam">sam</option>
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97 </param>
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98 <section name="adv" title="Advanced Options" expanded="False">
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99 <param name="header" type="select" value="yes">
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100 <label>output header</label>
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101 <option value="yes">Yes</option>
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102 <option value="no">No</option>
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103 </param>
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104 <expand macro="alignments"/>
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105 <expand macro="region"/>
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106 <expand macro="matepairDist"/>
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107 <param name="primary" type="select" value="no">
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108 <label>only primary aligments</label>
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109 <option value="no">No</option>
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110 <option value="yes">Yes</option>
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111 </param>
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112 <expand macro="minMapq"></expand>
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113 </section>
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114 </inputs>
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115 <outputs>
1
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116 <collection name="output_collection" type='list'>
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117 <filter>input['input_select'] == "file_list"</filter>
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118 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
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119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
2
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120 </collection>
0
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121 <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
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122 <filter>input['input_select'] == "accession_number"</filter>
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123 <change_format>
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124 <when input="outputformat" value="sam" format="sam"/>
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125 </change_format>
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126 </data>
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127 <data name="output_file" format="bam" label="${input.file.name}.${outputformat}">
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128 <filter>input['input_select'] == "file"</filter>
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129 <change_format>
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130 <when input="outputformat" value="sam" format="sam"/>
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131 </change_format>
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132 </data>
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133 </outputs>
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134 <tests>
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135 <test>
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136 <param name="input_select" value="accession_number"/>
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137 <param name="accession" value="SRR925743"/>
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138 <param name="outputformat" value="sam"/>
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139 <param name="region" value="17:41243452-41277500"/>
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140 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/>
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141 </test>
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142 </tests>
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143 <help>
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144 This tool extracts reads from sra archives using sam-dump.
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145 The sam-dump program is developed at NCBI, and is available at
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146 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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147 @SRATOOLS_ATTRRIBUTION@
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148 </help>
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149 <expand macro="citation"/>
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150 </tool>