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1 <tool id="rna_probing_plot" version="1.0.0" name="RNA Plot" force_history_refresh="True">
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2
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3 <description></description>
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4 <requirements>
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5 <requirement type="package" version="3.1.1">R_3_1_1</requirement>
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6 <requirement type="R-module">RNAprobR</requirement>
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7 <requirement type="package" version="1.0.0">RNAprobR</requirement>
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8 <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement>
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9 </requirements>
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10
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11 <command interpreter="Rscript">
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12 plot_rna.R -i $input -t "$transcript" -m $norm_method -c $cutoff -p $plot_type -o $plot > /dev/null
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13 </command>
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14
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15 <inputs>
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16 <param name="input" type="data" format="tabular" label="Input dataset" help="'Normalize' tool tabular output." />
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17
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18 <param name="transcript" type="text" size="20" label="Transcript identifier" help="Select the transcript that the plot should be generated for.">
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19 <validator type="empty_field"/>
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20 </param>
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21 <param name="norm_method" type="select" display="checkboxes" multiple="true" label="Normalization method" help="Column values to be ploted (One plot per selected method).">
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22 <option value="dtcr">deltaTCR</option>
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23 <option value="slograt">Smooth Log2 Ratio</option>
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24 <option value="swinsor">Sliding window Winsorization</option>
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25 <option value="TC.treated">Termination Count (Treated)</option>
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26 <option value="Cover.treated">Coverage (Treated)</option>
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27 <option value="TCR.treated">TCR (Treated)</option>
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28 <option value="TC.control">Termination Count (Control)</option>
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29 <option value="Cover.control">Coverage (Control)</option>
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30 <option value="TCR.control">TCR (Control)</option>
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31 </param>
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32 <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." />
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33 <param name="plot_type" type="select" label="Plot type">
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34 <option value="l">Lines</option>
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35 <option value="h">Histogram</option>
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36 </param>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="plot" format="pdf" label="${tool.name} on ${on_string}: ${transcript} plot" />
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 </test>
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46 </tests>
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47
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48 <help>
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49 **What it does**
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50
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51 Produces plots for a given transcript in the tabular file produced by *Normalize* tool (one plot per selected method). If a selected normalizing method is not included in the input file it simply not be plotted.
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52
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53 ------
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54
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55 **Example**
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56
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57 Input (head)::
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58
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59 RNAid Pos nt dtcr dtcr.p
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60 16S_rRNA_E.coli 1 A 0 0.00787957002462928
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61 16S_rRNA_E.coli 2 A 0.000606618229204106 2.87738710042044e-07
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62 16S_rRNA_E.coli 3 A 0.00170457733442839 0.0242502062681708
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63 16S_rRNA_E.coli 4 T 0.00171914631528914 0.504983784068465
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64 16S_rRNA_E.coli 5 T 0.00111252808608504 5.26073688354678e-06
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65 16S_rRNA_E.coli 6 G 0.00175507669063296 9.92896700324683e-05
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66
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67 Output (Significance: 1e-08, type: histogram)
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68
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69 .. image:: http://people.binf.ku.dk/slm279/plot.png
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70
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71 </help>
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72 </tool>
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