|
0
|
1 <tool id="vsttransform" name="Variance stabilizing transformation" version="1.0.0">
|
|
|
2 <description>
|
|
|
3 using DESeq
|
|
|
4 </description>
|
|
|
5
|
|
|
6 <requirements>
|
|
|
7 <requirement type="package" version="3.0.1">package_r3</requirement>
|
|
|
8 <requirement type="package" version="1.0.0">r_additions</requirement>
|
|
|
9 <requirement type="package" version="2.12">biocbasics</requirement>
|
|
|
10 </requirements>
|
|
|
11
|
|
|
12 <command interpreter="perl">
|
|
|
13 vst_transformation.pl ${parameters}
|
|
|
14 </command>
|
|
|
15
|
|
|
16 <inputs>
|
|
|
17 <param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count on mapped RNA-seq data" />
|
|
|
18 <param name="header_row" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the table has a header row" />
|
|
|
19 <param name="header_columns" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the first column contains identifiers" />
|
|
|
20
|
|
|
21 <repeat name="replicates" title="Replicate group">
|
|
|
22 <param name="repl_group_name" type="text" value="" size="50" label="Replicate group name">
|
|
|
23 <sanitizer invalid_char="">
|
|
|
24 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
|
|
|
25 </sanitizer>
|
|
|
26 </param>
|
|
|
27 <param name="rep_columns" label="Select replicates" type="data_column" data_ref="counttable" numerical="True"
|
|
|
28 multiple="true" use_header_names="true" size="120" display="checkboxes">
|
|
|
29 <validator type="no_options" message="Please select at least one column."/>
|
|
|
30 </param> <!-- $replicates contains a comma-separated list of number -->
|
|
|
31 </repeat>
|
|
|
32 </inputs>
|
|
|
33
|
|
|
34 <outputs>
|
|
|
35 <data format="tabular" name="outtab" label="${tool.name} of ${on_string}"/>
|
|
|
36 <data format="html" name="html_file" label="Histogram of ${tool.name} of ${on_string}"/>
|
|
|
37 </outputs>
|
|
|
38
|
|
|
39 <configfiles>
|
|
|
40 <configfile name="parameters">
|
|
|
41 ## first we pass some galaxy environment variables
|
|
|
42 counttable==$counttable
|
|
|
43 header_row==$header_row
|
|
|
44 header_columns==$header_columns
|
|
|
45 outtab==$outtab
|
|
|
46 html_file==$html_file
|
|
|
47
|
|
|
48 ##REPEAT BLOCK
|
|
|
49 #for $i, $s in enumerate( $replicates )
|
|
|
50 replicates_$s.repl_group_name==$s.rep_columns
|
|
|
51 #end for
|
|
|
52 </configfile>
|
|
|
53
|
|
|
54 </configfiles>
|
|
|
55
|
|
|
56 <tests>
|
|
|
57 <test>
|
|
|
58 <param name="counttable" value="counttable1.tsv" ftype="tabular" />
|
|
|
59 <param name="header_row" value="TRUE" />
|
|
|
60 <param name="header_columns" value="TRUE" />
|
|
|
61 <param name="repl_group_name" value="can" />
|
|
|
62 <param name="rep_columns" value="2,3" />
|
|
|
63 <output name="outtab" file="vst_transf_tabout.txt" ftype="tabular" />
|
|
|
64 <output name="html_file" file="vst_transf_htmlout.html" ftype="html" lines_diff="6"/>
|
|
|
65 </test>
|
|
|
66 </tests>
|
|
|
67
|
|
|
68 <help>
|
|
|
69 **Variance stabilizing transformation**
|
|
|
70
|
|
|
71 This tool takes in raw count data per feature and applies a variance stabilizing transformation using DESeq.
|
|
|
72 </help>
|
|
|
73 </tool>
|
