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1 <tool id="indel_table" name="Indel Analysis Table" version="1.0.0">
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2 <description>for combining indel interval data</description>
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3 <command interpreter="python">
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4 indel_table.py
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5 --input1=$input1
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6 --sum1=$sum1
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7 --input2=$input2
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8 --sum2=$sum2
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9 --output=$output1
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10 #for $i in $inputs
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11 ${i.input}
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12 ${i.sum}
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13 #end for
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14 </command>
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15 <inputs>
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16 <param format="interval" name="input1" type="data" label="Select first file to add" />
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17 <param name="sum1" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include first file's totals in overall total" />
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18 <param format="interval" name="input2" type="data" label="Select second file to add" />
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19 <param name="sum2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include second file's totals in overall total" />
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20 <repeat name="inputs" title="Input Files">
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21 <param name="input" label="Add file" type="data" format="interval" />
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22 <param name="sum" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include file's totals in overall total" />
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23 </repeat>
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24 </inputs>
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25 <outputs>
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26 <data format="interval" name="output1" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1" value="indel_table_in1.interval" ftype="interval" />
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31 <param name="sum1" value="true"/>
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32 <param name="input2" value="indel_table_in2.interval" ftype="interval" />
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33 <param name="sum2" value="true" />
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34 <param name="input" value="indel_table_in3.interval" ftype="interval" />
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35 <param name="sum" value="true" />
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36 <output name="output1" file="indel_table_out1.interval" ftype="interval" />
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37 </test>
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38 </tests>
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39 <help>
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40
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41 **What it does**
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42
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43 Creates a table allowing for analysis and comparison of indel data. Combines any number of interval files that have been produced by the tool that converts indel SAM data to interval format. Includes overall total counts for all or some files. The tool has the option to not include a given file's counts in the total column. This could be useful for combined data if the counts for certain indels might be included more than once.
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44
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45 The exact columns of the output will depend on the columns of the input. Here is the detailed specification of the output columns::
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46
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47 Column Description
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48 ------------------------------- ----------------------------------------------------------------------------------
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49 1 ... m "Indel" All the "indel" columns, which contain the info that will be checked for equality
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50 m + 1 Total Occurrences Total number of occurrences of this indel across all (included) files
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51 m + 2 Occurrences for File 1 Number of occurrences of this indel for first file
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52 m + 3 Occurrences for File 2 Number of occurrences of this indel for second file
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53 [m + ...] [...] [Number of occurrences of this indel for ... file]
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54
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55 The most likely columns would be from the output of the Convert SAM to Interval/BED tool, so: Chromosome, Start position, End position, I/D (Insertion/Deletion), -/<base(s)> (Deletion/Inserted base(s)), Total Occurrences (across files), Occurrences for File 1, Occurrences for File 2, etc. See below for an example.
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56
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57
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58 -----
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59
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60 **Example**
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61
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62 Suppose you have the following 4 files::
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63
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64 chrM 300 301 D - 6
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65 chrM 303 304 D - 19
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66 chrM 359 360 D - 1
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67 chrM 410 411 D - 1
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68 chrM 435 436 D - 1
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69
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70 chrM 410 411 D - 1
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71 chrM 714 715 D - 1
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72 chrM 995 997 D - 1
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73 chrM 1168 1169 I A 1
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74 chrM 1296 1297 D - 1
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75
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76 chrM 300 301 D - 8
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77 chrM 525 526 D - 1
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78 chrM 958 959 D - 1
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79 chrM 995 996 D - 3
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80 chrM 1168 1169 I C 1
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81 chrM 1296 1297 D - 1
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82
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83 chrM 303 304 D - 22
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84 chrM 410 411 D - 1
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85 chrM 435 436 D - 1
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86 chrM 714 715 D - 1
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87 chrM 753 754 I A 1
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88 chrM 1168 1169 I A 1
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89
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90 and the fifth file::
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91
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92 chrM 303 304 D - 22
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93 chrM 410 411 D - 2
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94 chrM 435 436 D - 1
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95 chrM 714 715 D - 2
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96 chrM 753 754 I A 1
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97 chrM 995 997 D - 1
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98 chrM 1168 1169 I A 2
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99 chrM 1296 1297 D - 1
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100
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101 The following will be produced if you include the first four files in the sum, but not the fifth::
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102
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103 chrM 300 301 D - 14 6 0 8 0 0
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104 chrM 303 304 D - 41 19 0 0 22 22
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105 chrM 359 360 D - 1 1 0 0 0 0
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106 chrM 410 411 D - 3 1 1 0 1 2
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107 chrM 435 436 D - 2 1 0 0 1 2
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108 chrM 525 526 D - 1 0 0 1 0 0
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109 chrM 714 715 D - 2 0 1 0 1 2
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110 chrM 753 754 I A 1 0 0 0 1 1
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111 chrM 958 959 D - 1 0 0 1 0 0
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112 chrM 995 996 D - 3 0 0 3 0 0
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113 chrM 995 997 D - 1 0 1 0 0 1
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114 chrM 1168 1169 I A 2 0 1 0 1 2
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115 chrM 1168 1169 I C 1 0 0 1 0 0
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116 chrM 1296 1297 D - 2 0 1 1 0 1
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117
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118 The first numeric column includes the total or the next four columns, but not the fifth.
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119
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120
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121 </help>
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122 </tool>
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