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1 <tool id="chromatra_t" name="Chromatra T" version="1.0.0">
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2 <description>for visualizing genome-wide chromatin modifications</description>
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3 <command interpreter="python">chromatrat.py $gffinput $feainput $imgformat $stepwidth '$classboundaries' $upstreamstretch $maxx $tickspacing '$title' $output</command>
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4 <inputs>
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5 <param name="gffinput" format="gff" type="data" label="Normalized enrichment scores"/>
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6 <param name="feainput" format="tabular" type="data" label="Feature descriptions"/>
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7 <param name="imgformat" type="select" label="Image format">
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8 <option value="svg" selected="true">svg</option>
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9 <option value="png">png</option>
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10 <option value="pdf">pdf</option>
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11 </param>
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12 <param name="stepwidth" type="integer" value="150" min="1" label="Bin size in bp" />
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13 <param name="classboundaries" type="text" value="1, 4, 16, 50, 200" size="30" label="Class boundaries" />
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14 <param name="upstreamstretch" type="integer" value="450" min="0" label="Number of bp upstream of feature start to be plotted" />
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15 <param name="maxx" type="integer" value="5000" label="Max bp to be plotted along x-coordinate. (Enter -1 for max feature length)"/>
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16 <param name="tickspacing" type="integer" value="1000" label="Tick spacing along x-coordinate" />
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17 <param name="title" type="text" value="" size="30" label="Plot title" />
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18 </inputs>
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19 <outputs>
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20 <data format="svg" name="output">
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21 <change_format>
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22 <when input="imgformat" value="png" format="png" />
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23 <when input="imgformat" value="pdf" format="pdf" />
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24 <when input="imgformat" value="svg" format="svg" />
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25 </change_format>
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26 </data>
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27 </outputs>
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28
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29 <requirements>
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30 <requirement type="python-module">matplotlib</requirement>
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31 </requirements>
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32
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33 <help>
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34 CHROMATRA T visualizes the enrichment of chromatin modification across genomic features (e.g. all transcripts of a genome) in an unbiased way by accounting for feature length.
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35 Furthermore, CHROMATRA T groups features based on a second characteristic (e.g. transcriptional frequency of transcripts).
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36
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37 -----
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38
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39 .. class:: infomark
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40
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41 **Normalized enrichment scores**
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42
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43 Enrichment scores must be provided in *GGFv3* format.
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44
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45 .. class:: infomark
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46
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47 **Feature descriptions**
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48
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49 Features must be provided in a *TAB*-delimited format in this order:
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50
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51 -1. feature name
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52
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53 -2. chromosome number
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54
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55 -3. strand
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56
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57 -4. feature start
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58
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59 -5. feature end
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60
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61 -6. feature attribute
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62
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63 .. class:: infomark
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64
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65 **Class boundaries**
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66
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67 Comma-seperated values spanning the *entire* numerical range of feature attributes. Values are interpreted as upper limits of the classes.
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68 Example: Assuming the feature attribute to be transcriptional frequency of transcripts and the attribute value range to be 0.1 up to 85.3 mRNA/h, a proper class boundary specification might look like: "1, 5, 10, 100".
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69 This would partition the range of transcriptional frequencies into 4 classes such that *class 1* would contain all transcripts less or equal to 1 mRNA/h, *class 2* all greater than 1 and less or equal to 5 mRNA/h, *class 3* all greater than 5 and less or equal 10 mRNA/h, and *class 4* all transcripts greater than 10 (and less than 100) mRNA/h.
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70
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71 .. class:: warningmark
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72
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73 The last boundary value must be greater or equal to the largest attribute value.
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74 </help>
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75
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76 </tool>
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