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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="crac" name="CRAC" version="1.0">
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3 <requirements>
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4 <requirement type='package' version="1.3.0">crac</requirement>
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5 </requirements>
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6 <description>Analyzing RNAs in high-throughput sequencing data</description>
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7 <command interpreter="bash"> crac_wrapper.sh
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8 #if $Genome.which_genome == "prebuilt"
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9 <!--1--> "$Genome.prebuilt_genome.fields.path"
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10 #else
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11 <!--1--> "$Genome.index_input.extra_files_path"
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12 #end if
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13 #if $condi_compressed == "yes"
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14 --gz
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15 #end if
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16 <!--2--> $output_name.extra_files_path <!-- Usefull for submitting jobs on crac.sh-->
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17 -r $input -k $kmer_length --read-length $read_length --sam $output_name
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18 #if $condi_deep_snp.deepSNP == "yes"
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19 --deep-snv --nb-nucleotides-snv-comparison $condi_deep_snp.nb_nucleotides_snp_comparison
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20 #end if
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21 #if $choixSettings.settings == "experimental"
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22 --max-splice-length $choixSettings.max_splice_length
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23 --max-bio-indel $choixSettings.max_bio_indel
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24 --min-duplication $choixSettings.min_duplication
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25 --max-duplication $choixSettings.max_duplication
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26 --min-percent-single-loc $choixSettings.min_percent_single_loc
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27 --min-percent-duplication-loc $choixSettings.min_percent_duplication_loc
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28 --max-bases-randomly-matched $choixSettings.max_bases_randomly_matched
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29 --max-extension-length $choixSettings.max_extension_length
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30 --min-support-no-cover $choixSettings.min_support_no_cover
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31 --min-break-length $choixSettings.min_break_length
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32 #end if
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33 #if str($detailed_sam) == "yes"
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34 --detailed-sam
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35 #end if
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36
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37 </command>
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38
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39 <inputs>
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40 <!-- Normal Setting -->
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41
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42 <conditional name="Genome"> <!-- Conditional 3 (Which genome) -->
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43 <param name="which_genome" type="select" label="Do you want to use a pre-built reference genome or a Crac-index generated genome from your history?" help="Pre-built reference genomes are generated by Crac-index.">
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44 <option value="prebuilt"> Use a pre-built reference genome </option>
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45 <option value="history"> Use a Crac-index generated genome from my history</option>
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46 </param>
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47
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48 <when value="prebuilt">
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49 <param name="prebuilt_genome" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact authors">
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50 <options from_data_table="crac_indexes">
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51 <filter type="sort_by" column="2" />
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52 <validator type="no_options" message="No indexes are available" />
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53 </options>
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54 </param>
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55 </when>
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56
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57 <when value="history">
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58 <param name="index_input" format="crac_index" type="data" label="Reference Genome" help="Select an indexed Genome from your history"/>
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59 </when>
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60 </conditional>
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61
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62
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63 <param name="input" format="txt,raw,fastq" type="data" label="Reads File" help="Select a file"/>
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64 <param name="kmer_length" type="integer" min="12" max="32" value="21" label="k-mer length">
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65 <help>k-mer length must be carefully chosen. A k-mer of that length must map to a unique location in the genome with a high probability. Recommended value for the human genome: 22</help>
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66 </param>
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67 <param name="read_length" type="integer" label="Read length" value="0" help="Set read length when all reads have the same length to dramatically increase computation speed. Default value (no read length considered) : 0. Note : If read length is set, shorter reads will be ignored, longer reads will be cut."/>
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68 <param name="detailed_sam" type="select" label="Do you want a detailed sam output file ?" help="Detailed sam output file gives you information on the SNPs, Splice junctions, Sequencing errors, Chimeras, ..." >
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69 <option value="no"> No, I do not want detailed sam output file </option>
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70 <option value="yes"> Yes, I want detailed sam output file </option>
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71 <when value="yes"/> <!-- Supress warnings-->
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72 <when value="no"/> <!-- Supress warnings-->
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73 </param>
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74 <param name="condi_compressed" type="select" display="radio" label="Compress output files?">
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75 <option value="yes">Yes</option>
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76 <option value="no">No</option>
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77 </param>
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78 <conditional name="condi_deep_snp"> <!-- Conditional 1 -->
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79 <param type="select" name="deepSNP" label="Search hard for SNPs?">
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80 <option value="no" selected="true"> No, do not search hard for SNVs </option>
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81 <option value="yes"> Yes, search hard for SNVs (takes more time) </option>
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82 </param>
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83 <when value="yes">
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84 <param name="nb_nucleotides_snp_comparison" type="integer" value="8" label="Number of nucleotides for SNV comparison" help="Default value for human genome : 8. A smaller value will find more SNVs, but will be less accurate."/>
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85 </when>
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86 <when value="no"/> <!-- Suppress warnings -->
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87 </conditional> <!-- End Conditional 1 -->
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88
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89 <!-- Experimental Setting-->
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90 <conditional name="choixSettings"> <!-- Conditional 2 (setting choice) -->
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91 <param name="settings" type="select" label="Advanced CRAC settings to use" help="If you want full control to optimize your experience, use Advanced Settings. Be careful, these settings are experimental and one single change can make Crac fail">
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92 <option value="normal" selected="true"> Normal settings </option>
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93 <option value="experimental"> Advanced Settings </option>
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94 </param>
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95 <when value="normal"/> <!-- Supress warnings-->
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96 <when value="experimental"> <!-- Supress warnings-->
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97 <param name="max_splice_length" type="integer" value="300000" label="Maximum splice length" help="Splices larger than this value, will not be considered as splices, but (if possible) as chimeras. Default value for human genome : 300,000 bp." />
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98 <param name="max_bio_indel" type="integer" value="15" label="Maximum indel length. Larger indels will be considered as splice junctions" help=" HELP. Default value for human genome : 15 bp." />
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99 <param name="min_duplication" type="integer" value="2" label="Minimum duplication occurrence" help=" Minimum number of k-mer occurrences in the genome to be considered as duplicated. Default value for human genome : 2." />
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100 <param name="max_duplication" type="integer" value="9" label="Maximum duplication occurrence" help=" Maximum number of k-mer occurrences to be considered as duplicated. Default value for human genome : 9." />
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101 <param name="min_percent_single_loc" type="float" value="0.15" label="Minimum unique location percentage" help=" Minimal percentage of k-mers that must be unique in the genome, to consider the read as unique. Default value for human genome : 0.15." />
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102 <param name="min_percent_duplication_loc" type="float" value="0.20" label="Minimum duplicated location percentage" help=" Minimal percentage of k-mers that must be duplicated in the genome, to consider the read as duplicated. Default value for human genome : 0.20." />
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103 <!--param name="min_percent_multiple_loc" type="float" value="0.20" label="Minimum percent multiple localisation" help=" HELP. Default value for human genome : 0.20." /-->
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104 <param name="max_bases_randomly_matched" type="integer" value="10" label="Maximum bases randomly matched" help=" Maximum number of bases that can be considered as randomly matched. Default value for human genome : 10." />
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105 <param name="max_bases_retrieved" type="integer" value="10" label="Maximum bases retrieved" help=" Maximum number of bases retrieved from the genome when outputting deletions. Default value for human genome : 10." />
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106 <param name="max_extension_length" type="integer" value="10" label="Maximum extension length" help=" Maximal number of nucleotides visited to extend a break and to make sure that the location is consistent. Default value for human genome : 10." />
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107 <param name="min_support_no_cover" type="float" value="1.30" label="Minimum suppot no cover" help=" Average coverage along the read to consider it as not covered. Default value for human genome : 1.30." />
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108 <param name="min_break_length" type="float" value="0.5" label="Minimum break length" help=" Breaks shorter than this ratio times the k-mer length will be considered as too short and will be merged if necessary. Default value for human genome : 0.5." />
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109 </when> <!-- End "when experimental" -->
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110 </conditional> <!-- End Conditional 2 -->
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111 </inputs>
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112
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113 <outputs>
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114 <data name="output_name" format="sam" label="${tool.name} on ${on_string}: mapped reads" />
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 </test>
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120 </tests>
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121
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122 <help>
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123 **What it does**
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124
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125 CRAC proposes a novel way of analyzing reads that integrates genomic locations
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126 and local coverage, and delivers all above mentioned predictions in a single
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127 step. CRAC uses a double k-mer profiling approach to detect candidate
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128 mutations, indels, splice or fusion junctions in each single read.
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129
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130 .. _CRAC: http://crac.gforge.inria.fr/
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131
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132 If you use this tool, please cite:
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133 - Philippe N., Salson M., Commes T., Rivals E., `"CRAC: an integrated approach to the analysis of RNA-seq reads"`__, Genome Biology (2013), 14:R30, doi: 10.1186/gb-2013-14-3-r30.
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134
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135 .. __: http://genomebiology.com/2013/14/3/R30/
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136
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137 ------
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138
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139 **Input formats**
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140
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141 CRAC accepts files in FASTA, FASTQ or any text format (txt, raw, ...).
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142
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143 ------
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144
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145 **Output**
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146
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147 The output is in SAM format. If you choose the detailed SAM output, CRAC adds several flags to tell more informations. You can see the details here: http://crac.gforge.inria.fr/index.php?id=sam-documentation
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148
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149
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150 ------
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151
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152 **Crac settings**
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153
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154 Main options are displayed at the top of the page. If you're an experimented user, you can choose to display
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155 the whole Crac setting. Most of the options in Crac have been implemented here.
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156
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157 ------
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158 crac 1.3.0 Compiled on Sep 13 2013.
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159
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160 -h, --help <none> print this help and exit
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161 -f, --full-help <none> print a complete help and exit
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162 -v <none> print version and exit
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163
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164 Mandatory arguments
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165 -i <FILE> set genome index file (without the extension filename)
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166 -r <FILE> [FILE2] set read file. Specify FILE2 in case of paired-end reads
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167 -k <INT> set k-mer length
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168 -o, --sam <FILE> set SAM output filename or print on STDOUT with "-o -" argument
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169
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170 Optional arguments
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171 * Protocol
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172 --stranded <none> set the read mapping with for a strand specific library (DEFAULT non-strand specific)
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173
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174 * Efficiency
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175 --nb-threads <INT> set the number of worker threads (DEFAULT 1)
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176 --read-length, -m <INT> set read length in case of all reads have the same length to optimize
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177 CPU and memory times
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178 --treat-multiple <none> consider alignments with multiple locations (>max-duplication) rather than considering a no-alignment in the SAM file
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179 --max-locs <INT> set the maximum number of locations on the reference index (DEFAULT 300)
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180
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181 * Accuracy
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182 --no-ambiguity <none> discard biological events (splice, snv, indel, chimera) which have several matches on the reference index
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183
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184
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185 Optional output arguments
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186 --all <FILE> set output base filename for all causes following
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187 --gz <none> all output files specified after this argument are gzipped
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188
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189 * Summary and statistics
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190 --summary <FILE> set output summary file
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191 * Mapping
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192 --single <FILE> set output single file
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193 --duplicate <FILE> set output duplication file
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194 --multiple <FILE> set output multiple file
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195 --none <FILE> set output none file
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196 --normal <FILE> set output normal file
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197 --almost-normal <FILE> set output almost normal file
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198
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199 * Biological causes
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200 --snv <FILE> set output SNV file
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201 --indel <FILE> set output short indel file
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202 --splice <FILE> set output splice junction file
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203 --weak-splice <FILE> set output coverless splice junction file
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204 --chimera <FILE> set output chimera junction file
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205 --paired-end-chimera <FILE> set output for paired-end chimera file
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206 --biological <FILE> set output bio-undetermined file
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207
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208 * Sequence errors
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209 --errors <FILE> set output sequence errors file
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210
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211 * Repetition
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212 --repeat <FILE> set output repetition file
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213
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214 * Other causes
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215 --undetermined <FILE> set output undetermined file
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216 --nothing <FILE> set output nothing file
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217
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218 Optional process for specific research
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219 --deep-snv <none> will search hard to find SNPs
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220 --stringent-chimera <none> will search chimeras with more accuracy (but less sensitivity)
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221
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222 Optional process launcher (once must be selected)
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223 * Exact matching tool
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224 --emt <none> launch CRAC-emt for exact mapping of short reads
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225
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226 * Server tool (for debugging)
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227 --server <none> launch CRAC server,the output arguments will
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228 not be taken into account
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229 --input-name-server <STRING> DEFAULT classify.fifo
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230 --output-name-server <STRING> DEFAULT classify.out.fifo
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231
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232 Additional settings for users
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233 * Sam output file
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234 --detailed-sam <none> more informations are added in SAM output file
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235
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236 * Mapping
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237 --min-percent-single-loc <FLOAT> DEFAULT 0.15
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238 --min-duplication <INT> DEFAULT 2
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239 --max-duplication <INT> DEFAULT 9
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240 --min-percent-duplication-loc <FLOAT> DEFAULT 0.15
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241 --min-percent-multiple-loc <FLOAT> DEFAULT 0.50
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242 --min-repetition <INT> DEFAULT 20
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243 --min-percent-repetition-loc <FLOAT> DEFAULT 0.20
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244 * Biological causes
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245 --max-splice-length <INT> DEFAULT 300000
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246 --max-paired-end-length <INT> DEFAULT 300000
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247 --max-bio-indel <INT> DEFAULT 15
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248 --max-bases-retrieved <INT> DEFAULT 15
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249 * Undetermined
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250 --min-support-no-cover <FLOAT> DEFAULT 1.30
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251
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252 Additional settings for advanced users
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253 * Break verification and fusion (merging mirage breaks)
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254 --min-break-length <FLOAT> DEFAULT 0.50
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255 --max-bases-randomly-matched <INT> DEFAULT 10
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256 --max-extension-length <INT> DEFAULT 10
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257
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258 * Threading
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259 --nb-tags-info-stored <INT> DEFAULT 1000
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260
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261 * Deep SNV search option
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262 --nb-nucleotides-snv-comparison <INT> DEFAULT 8
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263 </help>
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264
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265 </tool>
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