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comparison split_file_on_column.xml @ 0:ad6a989924ac draft

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author bgruening
date Tue, 17 Dec 2013 15:24:50 -0500
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1 <tool id="tp_split_on_column" name="Split file" force_history_refresh="True" version="0.1.1">
2 <description>according to the values of a column</description>
3 <requirements>
4 <requirement type="package" version="4.1.0">gnu_awk</requirement>
5 </requirements>
6 <command>
7 awk '{print > "primary_${outfile.id}_" \$$column "_visible_${infile.ext}" }' $infile;
8 echo 'Created' `ls -l | wc -l` 'files:' > $outfile;
9 ls -1 --hide="*_stdout" --hide="*_stderr" >> $outfile;
10 </command>
11
12 <inputs>
13 <param format="txt" name="infile" type="data" label="File to select" />
14 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
15 </inputs>
16
17 <outputs>
18 <data format="input" name="outfile" metadata_source="infile" label="${tool.name} on ${on_string}"/>
19 </outputs>
20 <tests>
21 <test>
22 </test>
23 </tests>
24 <help>
25
26 **What it does**
27
28 This tool splits a file into different smaller files using a specific column.
29 It will work like the group tool, but every group is saved to its own file.
30
31 -----
32
33 **Example**
34
35 Splitting on column 4 from this::
36
37 chr7 56632 56652 cluster 1
38 chr7 56736 56756 cluster 1
39 chr7 56761 56781 cluster 2
40 chr7 56772 56792 cluster 2
41 chr7 56775 56795 cluster 2
42
43 will produce 2 files with different clusters::
44
45 chr7 56632 56652 cluster 1
46 chr7 56736 56756 cluster 1
47
48
49 chr7 56761 56781 cluster 2
50 chr7 56772 56792 cluster 2
51 chr7 56775 56795 cluster 2
52
53
54 </help>
55 </tool>