Mercurial > repos > cmmt > chromatra
comparison chromatral.xml @ 4:4c9201237641
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| author | cmmt |
|---|---|
| date | Mon, 23 Jan 2012 05:24:51 -0500 |
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| 3:519e45d9539f | 4:4c9201237641 |
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| 1 <tool id="chromatra_l" name="Chromatra L" version="1.0.0"> | |
| 2 <description>for visualizing genome-wide chromatin modifications</description> | |
| 3 <command interpreter="python">chromatral.py $gffinput $feainput $imgformat $stepwidth $upstreamstretch $maxx $tickspacing '$title' $output</command> | |
| 4 <inputs> | |
| 5 <param name="gffinput" format="gff" type="data" label="Normalized enrichment scores"/> | |
| 6 <param name="feainput" format="tabular" type="data" label="Feature descriptions"/> | |
| 7 <param name="imgformat" type="select" label="Image format"> | |
| 8 <option value="svg" selected="true">svg</option> | |
| 9 <option value="png">png</option> | |
| 10 <option value="pdf">pdf</option> | |
| 11 </param> | |
| 12 <param name="stepwidth" type="integer" value="150" min="1" label="Bin size in bp" /> | |
| 13 <param name="upstreamstretch" type="integer" value="450" min="0" label="Number of bp upstream of feature start to be plotted" /> | |
| 14 <param name="maxx" type="integer" value="5000" label="Max bp to be plotted along x-coordinate. (Enter -1 for max feature length)"/> | |
| 15 <param name="tickspacing" type="integer" value="1000" label="Tick spacing along x-coordinate" /> | |
| 16 <param name="title" type="text" value="" size="30" label="Plot title" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="svg" name="output"> | |
| 20 <change_format> | |
| 21 <when input="imgformat" value="png" format="png" /> | |
| 22 <when input="imgformat" value="pdf" format="pdf" /> | |
| 23 <when input="imgformat" value="svg" format="svg" /> | |
| 24 </change_format> | |
| 25 </data> | |
| 26 </outputs> | |
| 27 | |
| 28 <requirements> | |
| 29 <requirement type="python-module">matplotlib</requirement> | |
| 30 </requirements> | |
| 31 | |
| 32 <help> | |
| 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. | |
| 34 | |
| 35 ----- | |
| 36 | |
| 37 .. class:: infomark | |
| 38 | |
| 39 **Normalized enrichment scores** | |
| 40 | |
| 41 Enrichment scores must be provided in *GGFv3* format. | |
| 42 | |
| 43 .. class:: infomark | |
| 44 | |
| 45 **Feature descriptions** | |
| 46 | |
| 47 Features must be provided in a *TAB*-delimited format in this order: | |
| 48 | |
| 49 -1. feature name | |
| 50 | |
| 51 -2. chromosome number | |
| 52 | |
| 53 -3. strand | |
| 54 | |
| 55 -4. feature start | |
| 56 | |
| 57 -5. feature end | |
| 58 </help> | |
| 59 | |
| 60 </tool> |