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/tools/indels/indel_table.xml

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