|
0
|
1 <tool id="rnastr_plot" version="0.1" name="RNA Plot" force_history_refresh="True">
|
|
|
2
|
|
|
3 <description></description>
|
|
|
4 <requirements />
|
|
|
5
|
|
|
6 <command>/home/nikos/software/R-3.1.1/bin/Rscript ~/galaxy-dist/tools/rna_probing/plot_rna.R -i $input -t "$transcript" -m $norm_method -c $cutoff -p $plot_type -o $plot > /dev/null </command>
|
|
|
7
|
|
|
8 <inputs>
|
|
|
9 <param name="input" type="data" format="tabular" label="Input dataset" help="'Normalize' tool tabular output." />
|
|
|
10
|
|
|
11 <param name="transcript" type="text" size="20" label="Transcript identifier" help="Select the transcript that the plot should be generated for.">
|
|
|
12 <validator type="empty_field"/>
|
|
|
13 </param>
|
|
|
14 <param name="norm_method" type="select" display="checkboxes" multiple="true" label="Normalization method" help="Column values to be ploted (One plot per selected method).">
|
|
|
15 <option value="dtcr">deltaTCR</option>
|
|
|
16 <option value="slograt">Smooth Log2 Ratio</option>
|
|
|
17 <option value="swinsor">Sliding window Winsorization</option>
|
|
|
18 <option value="TC.treated">Termination Count (Treated)</option>
|
|
|
19 <option value="Cover.treated">Coverage (Treated)</option>
|
|
|
20 <option value="TCR.treated">TCR (Treated)</option>
|
|
|
21 <option value="TC.control">Termination Count (Control)</option>
|
|
|
22 <option value="Cover.control">Coverage (Control)</option>
|
|
|
23 <option value="TCR.control">TCR (Control)</option>
|
|
|
24 </param>
|
|
|
25 <param name="cutoff" type="float" max="1.0" value="0.05" label="Significance level" help="Reports p-values or standard deviation (red asterisks) below the significance level. Set a negative value to print none." />
|
|
|
26 <param name="plot_type" type="select" label="Plot type">
|
|
|
27 <option value="l">Lines</option>
|
|
|
28 <option value="h">Histogram</option>
|
|
|
29 </param>
|
|
|
30 </inputs>
|
|
|
31
|
|
|
32 <outputs>
|
|
|
33 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: ${transcript} plot" />
|
|
|
34 </outputs>
|
|
|
35
|
|
|
36 <tests>
|
|
|
37 <test>
|
|
|
38 </test>
|
|
|
39 </tests>
|
|
|
40
|
|
|
41 <help>
|
|
|
42 </help>
|
|
|
43 </tool>
|
