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author jgarbe
date Wed, 27 Nov 2013 14:44:13 -0500
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1 <tool id="rgttable" name="Read Group Tracking Table" version="1.0">
2 <description>Generate FPKM tables from cuffdiff read_group_tracking files.</description>
3 <command interpreter="perl">
4 rgttable.pl
5 #if $column.selcol == 'yes':
6 -c $column.colnum
7 #end if
8 $rgt_in $rgt_out
9 </command>
10 <inputs>
11 <param name="rgt_in" type="data" format="tabular" label="Input file" />
12 <conditional name="column">
13 <param name="selcol" type="select" label="FPKM column" >
14 <option value="no" selected="true">Use column 7 for the value (default for FPKM)</option>
15 <option value="yes" >Select the column to use for the value</option>
16 </param>
17 <when value="no"/>
18 <when value="yes">
19 <param name="colnum" type="data_column" data_ref="rgt_in" numerical="true" optional="true" label="column" />
20 </when>
21 </conditional>
22 <!--
23 <param name="column" type="integer" value="7" label="Data column to keep (default 7)" />
24 -->
25 </inputs>
26 <stdio>
27 </stdio>
28 <outputs>
29 <data name="rgt_out" format="tabular" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="rgt_in" ftype="tabular" value="genes.read_group_tracking" />
34 <param name="selcol" value="no" />
35 <output name="rgt_out" file="genes.rgt.tsv" />
36 </test>
37 </tests>
38 <help>
39 This script converts read group tracking files produced by Cuffdiff into a format useful
40 for importing into other programs.
41 The output has a row for each tracking_id, with a column for tracking_id, and additional columns for each unique combination of condition and replicate.
42
43 This works with the isoforms, genes, cds, and tss_groups
44 read group tracking files generated by cuffdiff.
45
46 INPUT
47 A cuffdiff read_group_tracking file
48
49 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
50 tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
51 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
52 AES heart 0 1 1.15043 1.15043 18.1912 = OK
53 AES heart 1 1 0.800708 0.800708 18.5033 = OK
54 AES heart 2 4 2.96393 2.96393 68.5644 = OK
55 AES skeletal 0 0 0 0 0 = OK
56 AES skeletal 1 1 1.05362 1.05362 25.0567 = OK
57 AES skeletal 2 0 0 0 0 = OK
58 ============= =========== =========== =========== ===================== ===================== ========= ================ ========
59
60 OUTPUT
61
62 ============= ========= ========= ========= ============ ============ ============
63 tracking_id heart-0 heart-1 heart-2 skeletal-0 skeletal-1 skeletal-2
64 ============= ========= ========= ========= ============ ============ ============
65 AES 18.1912 18.5033 68.5644 0 25.0567 0
66 ============= ========= ========= ========= ============ ============ ============
67
68
69
70 </help>
71 </tool>