Mercurial > repos > iuc > colibread_commet

annotate macros.xml @ 4:8c53dc8b4adb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Mon, 17 Aug 2020 10:38:36 -0400
parents 291753bf4013
children d03353742508
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10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <macros>
4
8c53dc8b4adb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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2 <token name="@DISCOSNP_VERSION@">2.5.4</token>
8c53dc8b4adb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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4 <xml name="discosnp_requirements">
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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5 <requirements>
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8c53dc8b4adb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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6 <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
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7 </requirements>
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8 </xml>
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9
0
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10 <token name="@discosnp_single_reads@"><![CDATA[
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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11 #for $input in $input_type_options.list_reads
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12 #set $filename = os.path.basename(str($input)) + "." + $input.ext
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13 ln -sf '${input}' '${filename}' &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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14 echo '${filename}' >> input.lst &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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15 #end for
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16 ]]></token>
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0
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18 <token name="@discosnp_paired_reads@"><![CDATA[
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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19 #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
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1
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21 #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext
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22 ln -sf '${paired.forward}' '${filenameFWD}' &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1
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24 #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext
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25 ln -sf '${paired.reverse}' '${filenameREV}' &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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27 echo '${filenameFWD}' > "paired_${i}.lst" &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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28 echo '${filenameREV}' >> "paired_${i}.lst" &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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29 echo "paired_${i}.lst" >> input.lst &&
10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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10e0e74c83af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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31 #end for
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32 ]]></token>
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34 <xml name="discosnp_inputs">
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35 <conditional name="input_type_options">
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36 <param name="input_type" type="select" label="Input options">
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37 <option value="single">Single end reads</option>
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38 <option value="paired">Paired end reads</option>
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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39 <option value="mix">Both single and paired reads</option>
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40 </param>
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41 <when value="single">
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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42 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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43 </when>
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44 <when value="paired">
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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45 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" />
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46 </when>
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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47 <when value="mix">
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48 <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" />
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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49 <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/>
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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50 </when>
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51 </conditional>
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52 </xml>
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53
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54 <xml name="discosnp_options">
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55 <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/>
291753bf4013 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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56 <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/>
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57 <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" />
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58 <param argument="-k" type="integer" label="Size of kmers" value="31" />
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59
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60 <conditional name="coverage_options_type" >
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61 <param name="coverage_options" type="select" label="Coverage option">
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62 <option value="auto"></option>
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63 <option value="custom"></option>
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64 </param>
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65 <when value="auto" />
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66 <when value="custom">
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67 <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/>
1
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68 </when>
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69 </conditional>
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70
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71 <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" />
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72 <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" />
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73
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74 </xml>
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75
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76 <token name="@discosnp_inputs@"><![CDATA[
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77 -r input.lst
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78 -D ${D}
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79 -P ${P}
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80 ${low_complexity}
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81 -k ${k}
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82
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83 #if str($coverage_options_type.coverage_options) == 'auto'
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84 -c auto
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85 #else
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86 -c '${coverage_options_type.c}'
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87 #end if
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88 -C ${C}
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89 -d ${d}
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90 ]]></token>
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91
0
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92 <token name="@lordec_inputs@"><![CDATA[
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93 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
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94 -i '${program_type_choice.i}'
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95 -k ${program_type_choice.k}
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96 -s ${program_type_choice.s}
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97 ]]></token>
1
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98
0
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99 <xml name="lordec_inputs">
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100 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
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101 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
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102 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
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103 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
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104 </xml>
1
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105
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106 <token name="@discosnp_help@"><![CDATA[
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107 -------
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108
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109 .. class:: warningmark
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110
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111 **Input parameters**
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112
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113 -Sequences files in fasta or fastq each allele will be counted in each file individually
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114
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115 -Use collections: data list and/or data list paired
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116
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117 -Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
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118
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119 -------
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120
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121 .. class:: warningmark
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122
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123 **Ouput parameters**
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124
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125 -VCF file with coordinates on the higher branch sequences or on a reference genome if provided
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126
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127 -Fasta file with sequence extensions around the SNP.
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128
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129
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130 -------
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131
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132 **Web site**
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133
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134 https://colibread.inria.fr/software/discosnp/
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135
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136 ]]></token>
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137
0
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138 <xml name="citations">
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139 <citations>
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140 <yield/>
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141 <citation type="doi">10.1186/s13742-015-0105-2</citation>
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142 </citations>
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143 </xml>
1
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144
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145 <xml name="discosnp_citation">
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146 <citation type="doi">10.1101/209965</citation>
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147 </xml>
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148
0
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149 </macros>