Mercurial > repos > alermine > nebula
comparison [APliBio]Nebula tools suite/Nebula/MakeTSSdist/makeTSSdist_wrapper.xml @ 0:2ec3ba0e9e70 draft
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author | alermine |
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date | Thu, 25 Oct 2012 08:18:25 -0400 |
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-1:000000000000 | 0:2ec3ba0e9e70 |
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1 <tool id="makeTSSdist" name="MakeTSSdist" version="1.0"> | |
2 <description>Get peak distribution around TSS</description> | |
3 <command interpreter="bash"> | |
4 | |
5 #if str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "no" #makeTSSdist_wrapper.sh -f $inputfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPNG -l $left -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "no" and $use_control.use_control_selector == "yes" # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -o $outputPDF -l $left -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -p 0 #elif str( $if_PDF ) == '1' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "no" # makeTSSdist_wrapper.sh -f $inputfile -e $regfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -p 1 #elif str( $if_PDF ) == '0' and $use_reg.use_reg_selector == "yes" and $use_control.use_control_selector == "yes" #makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPNG -r $right -u $stats -v $input_organism.version -e $regfile -p 0 #else # makeTSSdist_wrapper.sh -f $inputfile -c $controlfile -l $left -o $outputPDF -r $right -u $stats -v $input_organism.version -e $regfile -p 1 #end if | |
6 </command> | |
7 <inputs> | |
8 | |
9 <param name="inputfile" type="data" label="ChIP peaks" value="ChIP peaks File" format="bed"/> | |
10 | |
11 | |
12 <conditional name="use_control"> | |
13 <param name="use_control_selector" type="select" label="Use control data"> | |
14 <option value="no" selected="true">No</option> | |
15 <option value="yes">Yes</option> | |
16 </param> | |
17 <when value="yes"> | |
18 <param name="controlfile" type="data" label="Control peaks" value="Control peaks File" format="bed"/> | |
19 </when> | |
20 </conditional> | |
21 | |
22 <param name="left" type="integer" label="Step (bp)" value="1000"/> | |
23 <param name="right" type="integer" label="length of the region +-TSS to consider (bp)" value="50000"/> | |
24 | |
25 <conditional name="input_organism"> | |
26 <param name="input_organism_selector" type="select" label="Select organism"> | |
27 <option value="Human" selected="true">Homo sapiens</option> | |
28 <option value="Mouse">Mus musculus</option> | |
29 <option value="Zebrafish">Zebrafish (Danio rerio)</option> | |
30 <option value="XTropicalis">X.Tropicalis</option> | |
31 <option value="Bacteria/MycoTube">M. tuberculosis</option> | |
32 </param> | |
33 <when value="Human"> | |
34 <param name="version" type="select" label="Select genome vesion"> | |
35 <option value="hg19" selected="true">hg19</option> | |
36 <option value="hg18">hg18</option> | |
37 </param> | |
38 </when> | |
39 <when value="Mouse"> | |
40 <param name="version" type="select" label="Select genome vesion"> | |
41 <option value="mm8" >mm8</option> | |
42 <option value="mm9" selected="true">mm9</option> | |
43 <option value="mm10" >mm10</option> | |
44 </param> | |
45 </when> | |
46 <when value="Zebrafish"> | |
47 <param name="version" type="select" label="Select genome vesion"> | |
48 <option value="zv9" selected="true">zv9</option> | |
49 </param> | |
50 </when> | |
51 <when value="XTropicalis"> | |
52 <param name="version" type="select" label="Select genome vesion"> | |
53 <option value="xenTro2" >xenTro2</option> | |
54 <option value="xenTro3" selected="true">xenTro3</option> | |
55 </param> | |
56 </when> | |
57 <when value="Bacteria/MycoTube"> | |
58 <param name="version" type="select" label="Select genome vesion"> | |
59 <option value="H37Rv" selected="true">H37Rv</option> | |
60 </param> | |
61 </when> | |
62 </conditional> | |
63 <conditional name="use_reg"> | |
64 <param name="use_reg_selector" type="select" label="Use transcriptomic data (up- and down- regulated genes)"> | |
65 <option value="no" selected="true">No</option> | |
66 <option value="yes">Yes</option> | |
67 </param> | |
68 <when value="yes"> | |
69 <param name="regfile" type="data" label="File with information about gene regulation" value="Regulation data" format="txt"/> | |
70 </when> | |
71 </conditional> | |
72 | |
73 <param name="if_PDF" type="boolean" label="Do you want to have a PDF image (default PNG)?" truevalue="1" falsevalue="0" checked="False"/> | |
74 </inputs> | |
75 <outputs> | |
76 <data name="outputPNG" format="png" label="Peak location distribution (png)"> | |
77 <filter>(if_PDF == 0)</filter> | |
78 </data> | |
79 <data name="outputPDF" format="pdf" label="Peak location distribution (pdf)"> | |
80 <filter>(if_PDF == True)</filter> | |
81 </data> | |
82 <data name="stats" format="tabular" label="Peak location distribution (stats)"/> | |
83 </outputs> | |
84 <help> | |
85 **What it does** | |
86 | |
87 This tool creates a .png file with distribution of peaks around gene TSS | |
88 | |
89 </help> | |
90 </tool> |