Mercurial > repos > devteam > picard
annotate picard_CollectAlignmentSummaryMetrics.xml @ 3:52fdfc45590a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 16 Jul 2015 15:32:31 -0400 |
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children | 2589e6207cb4 |
rev | line source |
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3
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0"> |
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2 <description>writes a file containing summary alignment metrics</description> |
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3 <macros> |
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4 <import>picard_macros.xml</import> |
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5 </macros> |
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6 <expand macro="requirements" /> |
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7 <command> |
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8 @java_options@ |
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9 ##set up input files |
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10 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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11 #set $reference_fasta_filename = "localref.fa" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 #if str( $reference_source.reference_source_selector ) == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 #else: |
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16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 #end if |
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18 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 java -jar \$JAVA_JAR_PATH/picard.jar |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 CollectAlignmentSummaryMetrics |
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21 INPUT="${inputFile}" |
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22 OUTPUT="${outFile}" |
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23 MAX_INSERT_SIZE=${maxinsert} |
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24 #for $sequence in $adapters: |
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25 ADAPTER_SEQUENCE="${sequence.adapter}" |
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26 #end for |
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27 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 IS_BISULFITE_SEQUENCED="${bisulphite}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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32 ASSUME_SORTED="${assume_sorted}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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33 |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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34 VALIDATION_STRINGENCY="${validation_stringency}" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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35 QUIET=true |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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36 VERBOSITY=ERROR |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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37 |
52fdfc45590a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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38 </command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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39 <inputs> |
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40 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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41 <conditional name="reference_source"> |
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42 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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43 <option value="cached">Local cache</option> |
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44 <option value="history">History</option> |
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45 </param> |
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46 <when value="cached"> |
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47 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> |
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48 <options from_data_table="all_fasta"> |
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49 </options> |
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50 <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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51 </param> |
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52 </when> |
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53 <when value="history"> |
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54 <param name="ref_file" type="data" format="fasta" label="Use the following 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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55 </when> |
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56 </conditional> |
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57 <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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58 <option value="ALL_READS" selected="True">All reads</option> |
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59 <option value="SAMPLE">Sample</option> |
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60 <option value="LIBRARY">Library</option> |
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61 <option value="READ_GROUP">Read group</option> |
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62 </param> |
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63 <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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64 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> |
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65 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> |
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66 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> |
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67 </repeat> |
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68 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/> |
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69 |
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70 <expand macro="VS" /> |
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71 |
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72 </inputs> |
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73 |
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74 <outputs> |
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75 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> |
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76 </outputs> |
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77 |
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78 <stdio> |
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79 <exit_code range="1:" level="fatal"/> |
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80 </stdio> |
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81 |
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82 |
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83 <tests> |
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84 <test> |
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85 <param name="bisulphite" value="false" /> |
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86 <param name="sorted" value="true" /> |
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87 <param name="adaptors" value="" /> |
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88 <param name="maxinsert" value="100000" /> |
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89 <param name="reference_source_selector" value="history" /> |
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90 <param name="ref_file" value="picard_CASM_ref.fa" /> |
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91 <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> |
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92 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> |
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93 </test> |
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94 </tests> |
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95 |
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96 <help> |
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97 |
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98 .. class:: infomark |
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99 |
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100 **Purpose** |
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101 |
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102 Reads a SAM or BAM file and writes a file containing summary alignment metrics. |
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103 |
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104 @dataset_collections@ |
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105 |
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106 @description@ |
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107 |
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108 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with |
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109 inter-chromosomal pairs. Default value: 100000. |
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110 |
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111 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may |
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112 be specified 0 or more times. |
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113 |
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114 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel |
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115 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, |
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116 LIBRARY, READ_GROUP} This option may be specified 0 or more times. |
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117 |
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118 IS_BISULFITE_SEQUENCED=Boolean |
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119 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. |
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120 |
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121 |
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122 REFERENCE_SEQUENCE=File |
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123 R=File Reference sequence fasta Default value: null. |
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124 |
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125 ASSUME_SORTED=Boolean |
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126 AS=Boolean If true (default), then the sort order in the header file will be ignored. |
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127 |
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128 @more_info@ |
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129 |
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130 </help> |
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131 </tool> |
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132 |
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133 |