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1 <tool id ="pyCalculateMutationFrequencies" name="pyCalculateMutationFrequencies">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pyCalculateMutationFrequencies.py
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7 -r $readdatafile
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8 -i $intervaldatafile
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9 -c $addChr.chr
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10 -o $output
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11 --mutsfreq $mutsfreq
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12 </command>
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13 <version_command>/usr/local/bin/pyCalculateMutationFrequencies.py --version</version_command>
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14 <inputs>
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15 <param format="gff" name="readdatafile" type="data" label="GFF Reads File --readdatafile" help="GFF file containing read data" />
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16 <param format="gtf" name="intervaldatafile" type="data" label="GFF Interval File --intervaldatafile" help="GFF file containing interval co-ordinates"/>
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17 <conditional name="addChr">
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18 <param name="chrfile" type="select" label="Choose Chromosome length file from">
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19 <option value="default" selected="true">Defaults</option>
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20 <option value="other">History</option>
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21 </param>
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22 <when value="default">
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23 <param name="chr" type="select" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes.Use pyCrac utility pyCalculateChromosomeLengths to create.">
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24 <options from_data_table="pycrac_chr"/>
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25 </param>
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26 </when>
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27 <when value="other">
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28 <param format="tabular" name="chr" type="data" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes"/>
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29 </when>
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30 </conditional>
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31
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32 <param format="integer" name="mutsfreq" type="integer" label="Minimum mutation frequency --mutsfreq " value="0" size="10" help="sets the minimal mutations frequency for an interval that you want to have written to our output file">
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33 <validator type="in_range" min="0" message="Please enter a value >= 0"/>
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34 </param>
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35 <param name="label" type="text" format="txt" size="30" value="pyCalculateMutationFrequencies" label="Enter output file label -o" />
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36 </inputs>
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37 <outputs>
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38 <data format="gtf" name="output" label="${label.value}.gtf"/>
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39 </outputs>
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **pyCalculateMutationFrequencies**
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45
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46 pyCalculateMutationFrequencies is part of the pyCRAC_ package. Takes an interval file and a pyReadCounters GTF file and calculates (cross-linking induced) mutation frequencies fore each interval.
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47 This tool can be used to calculate mutation frequencies for significant intervals (pyCalculateFDRs output file) or over-represented motifs (pyMotif GTF output file).
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48 It expects a pyCRAC GTF count_output_reads.gtf file and a GTF file with the intervals.
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49
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50 For example::
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51
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52 This pyCalculateFDRs GTF output file::
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53
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54 ##gff-version 2
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55 # generated by pyCalculateFDRs version 0.0.3, Sat Jun 1 21:16:23 2013
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56 # pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05
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57 # chromosome feature source start end minimal_coverage strand . attributes
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58 chrII protein_coding exon 203838 203887 3 + . gene_id "YBL011W"; gene_name "SCT1";
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59 chrII intergenic_region exon 407669 407708 3 + . gene_id "INT_0_445"; gene_name "INT_0_445";
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60 chrII intergenic_region exon 585158 585195 2 + . gene_id "INT_0_562"; gene_name "INT_0_562";
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61 chrII protein_coding exon 372390 372433 4 - . gene_id "YBR067C"; gene_name "TIP1";
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62 chrII intergenic_region exon 380754 380815 6 - . gene_id "INT_0_431"; gene_name "INT_0_431";
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63 chrIII protein_coding exon 138001 138044 5 + . gene_id "YCR012W"; gene_name "PGK1";
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64 chrIII intergenic_region exon 227997 228036 5 + . gene_id "INT_0_885"; gene_name "INT_0_885";
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65 chrIII intergenic_region exon 227997 228037 4 + . gene_id "INT_0_887"; gene_name "INT_0_887";
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66 chrIII tRNA exon 227997 228037 4 + . gene_id "tS(CGA)C"; gene_name "SUP61";
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67
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68 Will be converted into::
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69
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70 ##gff-version 2
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71 # generated by pyCalculateFDRs version 0.0.3, Sat Jun 1 21:16:23 2013
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72 # /Library/Frameworks/EPD64.framework/Versions/Current/bin/pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05
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73 # chromosome feature source start end minimal_coverage strand . attributes
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74 chrII protein_coding exon 203838 203887 3 + . gene_id "YBL011W"; gene_name "SCT1"; # 203882D33.3,203883D33.3,203884D33.3;
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75 chrII intergenic_region exon 407669 407708 3 + . gene_id "INT_0_445"; gene_name "INT_0_445"; # 407680D33.3,407681D33.3;
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76 chrII intergenic_region exon 585158 585195 2 + . gene_id "INT_0_562"; gene_name "INT_0_562"; # 585171D100.0,585172D100.0,585173D100.0;
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77 chrII protein_coding exon 372390 372433 4 - . gene_id "YBR067C"; gene_name "TIP1"; # 372412D50.0,372413D50.0;
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78 chrII intergenic_region exon 380754 380815 6 - . gene_id "INT_0_431"; gene_name "INT_0_431"; # 380786D90.2,380787D90.2;
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79 chrIII protein_coding exon 138001 138044 5 + . gene_id "YCR012W"; gene_name "PGK1"; # 138025D40.0,138026D30.0,138027D40.0;
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80 chrIII intergenic_region exon 227997 228036 5 + . gene_id "INT_0_885"; gene_name "INT_0_885"; # 228006D85.7,228007D100.0;
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81 chrIII intergenic_region exon 227997 228037 4 + . gene_id "INT_0_887"; gene_name "INT_0_887"; # 228006D85.7,228007D100.0;
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82 chrIII tRNA exon 227997 228037 4 + . gene_id "tS(CGA)C"; gene_name "SUP61"; # 228006D85.7,228007D100.0;
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83
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84
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85 The hash character at the end of each line (#) shows chromosomal coordinates of mutated nucleotides within the cluster interval and their mutation frequencies.
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86
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87 For example::
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88
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89 # 228007D100.0
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90
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91 indicates that 100% of the nucleotides in position 228007 were deleted in the interval.
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92
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93 By setting the --mutsfreq flag you can set a limit for the lowest mutation frequency that you want to have reported.
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94 This makes it relatively easy to select those significant regions that have nucleotides with high mutation frequencies.
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95
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96 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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97
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98 ------
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99
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100 **Parameter list**
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101
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102 Options::
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103
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104 -i intervals.gtf, --intervaldatafile=intervals.gtf
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105 provide the path to your GTF interval data file.
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106 -r reads.gtf, --readdatafile=reads.gtf
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107 provide the path to your GTF read data file.
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108 -c yeast.txt, --chromfile=yeast.txt
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109 Location of the chromosome info file. This file should
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110 have two columns: first column is the names of the
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111 chromosomes, second column is length of the
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112 chromosomes. Default is yeast
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113 -o intervals_with_muts.gtf, --output_file=intervals_with_muts.gtf
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114 provide a name for an output file. By default it
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115 writes to the standard output
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116 --mutsfreq=10, --mutationfrequency=10
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117 sets the minimal mutations frequency for an interval
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118 that you want to have written to our output file.
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119 Default = 0%. Example: if the mutsfrequency is set at
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120 10 and an interval position has a mutated in less than
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121 10% of the reads,then the mutation will not be
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122 reported.
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123
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124
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125 </help>
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126 </tool> |
