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1 <tool id="chromatra_l" name="Chromatra L" 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">chromatral.py $gffinput $feainput $imgformat $stepwidth $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="upstreamstretch" type="integer" value="450" min="0" label="Number of bp upstream of feature start to be plotted" />
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14 <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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15 <param name="tickspacing" type="integer" value="1000" label="Tick spacing along x-coordinate" />
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16 <param name="title" type="text" value="" size="30" label="Plot title" />
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17 </inputs>
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18 <outputs>
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19 <data format="svg" name="output">
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20 <change_format>
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21 <when input="imgformat" value="png" format="png" />
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22 <when input="imgformat" value="pdf" format="pdf" />
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23 <when input="imgformat" value="svg" format="svg" />
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24 </change_format>
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25 </data>
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26 </outputs>
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27
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28 <requirements>
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29 <requirement type="python-module">matplotlib</requirement>
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30 </requirements>
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31
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32 <help>
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33 CHROMATRA L 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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34
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35 -----
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36
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37 .. class:: infomark
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38
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39 **Normalized enrichment scores**
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40
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41 Enrichment scores must be provided in *GGFv3* format.
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42
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43 .. class:: infomark
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44
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45 **Feature descriptions**
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46
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47 Features must be provided in a *TAB*-delimited format in this order:
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48
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49 -1. feature name
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50
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51 -2. chromosome number
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52
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53 -3. strand
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54
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55 -4. feature start
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56
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57 -5. feature end
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58 </help>
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59
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60 </tool>
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