Mercurial > repos > bgruening > hicexplorer_hicpca
annotate macros.xml @ 0:61165fbb020d draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author | bgruening |
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date | Sat, 30 Dec 2017 09:14:06 -0500 |
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children | d5a86de86846 |
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61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <macros> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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3 <token name="@WRAPPER_VERSION@">2.0</token> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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4 <xml name="requirements"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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5 <requirements> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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7 <yield /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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8 </requirements> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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9 <version_command>@BINARY@ --version</version_command> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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10 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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11 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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12 <xml name="citations"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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13 <citations> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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14 <citation type="doi">10.5281/zenodo.1123667</citation> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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15 <yield /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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16 </citations> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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17 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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18 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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19 <xml name="zMax"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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20 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow --> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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21 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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22 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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23 <xml name="colormap"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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24 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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25 <option value="RdYlBu">RdYlBu</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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26 <option value="Accent">Accent</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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27 <option value="Spectral">Spectral</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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28 <option value="Set1">Set1</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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29 <option value="Set2">Set2</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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30 <option value="Set3">Set3</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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31 <option value="Dark2">Dark2</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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32 <option value="Reds">Reds</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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33 <option value="Oranges">Oranges</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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34 <option value="Greens">Greens</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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35 <option value="Blues">Blues</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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36 <option value="Greys">Greys</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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37 <option value="Purples">Purples</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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38 <option value="Paired">Paired</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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39 <option value="Pastel1">Pastel1</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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40 <option value="Pastel2">Pastel2</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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41 <option value="spring">spring</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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42 <option value="summer">summer</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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43 <option value="autumn">autumn</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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44 <option value="winter">winter</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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45 <option value="hot">hot</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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46 <option value="coolwarm">coolwarm</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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47 <option value="cool">cool</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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48 <option value="seismic">seismic</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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49 <option value="terrain">terrain</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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50 <option value="ocean">ocean</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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51 <option value="rainbow">rainbow</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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52 <option value="bone">bone</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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53 <option value="flag">flag</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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54 <option value="prism">prism</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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55 <option value="cubehelix">cubehelix</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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56 <option value="binary">binary</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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57 <option value="pink">pink</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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58 <option value="gray">gray</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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59 <option value="copper">copper</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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60 <option value="BrBG">BrBG</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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61 <option value="BuGn">BuGn</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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62 <option value="BuPu">BuPu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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63 <option value="GnBu">GnBu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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64 <option value="OrRd">OrRd</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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65 <option value="PiYG">PiYG</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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66 <option value="PRGn">PRGn</option> |
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67 <option value="PuOr">PuOr</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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68 <option value="PuRd">PuRd</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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69 <option value="PuBu">PuBu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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70 <option value="RdBu">RdBu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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71 <option value="RdGy">RdGy</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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72 <option value="RdPu">RdPu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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73 <option value="YlGn">YlGn</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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74 <option value="PuBuGn">PuBuGn</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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75 <option value="RdYlGn">RdYlGn</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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76 <option value="YlGnBu">YlGnBu</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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77 <option value="YlOrBr">YlOrBr</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
78 <option value="YlOrRd">YlOrRd</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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diff
changeset
|
79 <option value="gist_gray">gist_gray</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
80 <option value="gist_stern">gist_stern</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
81 <option value="gist_earth">gist_earth</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
82 <option value="gist_yarg">gist_yarg</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
83 <option value="gist_ncar">gist_ncar</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
84 <option value="gist_rainbow">gist_rainbow</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
85 <option value="gist_heat">gist_heat</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
86 <option value="gnuplot">gnuplot</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff
changeset
|
87 <option value="gnuplot2">gnuplot2</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
88 <option value="CMRmap">CMRmap</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff
changeset
|
89 <option value="bwr">bwr</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
90 <option value="hsv">hsv</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff
changeset
|
91 <option value="brg">brg</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
92 <option value="jet">jet</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
93 <option value="afmhot">afmhot</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
94 <option value="Accent_r">Accent reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
95 <option value="Spectral_r">Spectral reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
96 <option value="Set1_r">Set1 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
97 <option value="Set2_r">Set2 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
98 <option value="Set3_r">Set3 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
99 <option value="Dark2_r">Dark2 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
100 <option value="Reds_r">Reds reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
101 <option value="Oranges_r">Oranges reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
102 <option value="Greens_r">Greens reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff
changeset
|
103 <option value="Blues_r">Blues reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
104 <option value="Greys_r">Greys reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
105 <option value="Purples_r">Purples reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
106 <option value="Paired_r">Paired reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
107 <option value="Pastel1_r">Pastel1 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
108 <option value="Pastel2_r">Pastel2 reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
109 <option value="spring_r">spring reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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changeset
|
110 <option value="summer_r">summer reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
111 <option value="autumn_r">autumn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
112 <option value="winter_r">winter reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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changeset
|
113 <option value="hot_r">hot reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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diff
changeset
|
114 <option value="coolwarm_r">coolwarm reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
115 <option value="cool_r">cool reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
116 <option value="seismic_r">seismic reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
117 <option value="terrain_r">terrain reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
118 <option value="ocean_r">ocean reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
119 <option value="rainbow_r">rainbow reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
120 <option value="bone_r">bone reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
121 <option value="flag_r">flag reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
122 <option value="prism_r">prism reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
123 <option value="cubehelix_r">cubehelix reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
124 <option value="binary_r">binary reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
125 <option value="pink_r">pink reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
126 <option value="gray_r">gray reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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changeset
|
127 <option value="copper_r">copper reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
128 <option value="BrBG_r">BrBG reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
129 <option value="BuGn_r">BuGn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
130 <option value="BuPu_r">BuPu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
131 <option value="GnBu_r">GnBu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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changeset
|
132 <option value="OrRd_r">OrRd reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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changeset
|
133 <option value="PiYG_r">PiYG reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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changeset
|
134 <option value="PRGn_r">PRGn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
135 <option value="PuOr_r">PuOr reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
136 <option value="PuRd_r">PuRd reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
137 <option value="PuBu_r">PuBu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
138 <option value="RdBu_r">RdBu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
139 <option value="RdGy_r">RdGy reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
140 <option value="RdPu_r">RdPu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
141 <option value="YlGn_r">YlGn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
142 <option value="PuBuGn_r">PuBuGn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
143 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
144 <option value="RdYlGn_r">RdYlGn reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
145 <option value="YlGnBu_r">YlGnBu reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
146 <option value="YlOrBr_r">YlOrBr reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
147 <option value="YlOrRd_r">YlOrRd reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
148 <option value="gist_gray_r">gist_gray reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
149 <option value="gist_stern_r">gist_stern reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
150 <option value="gist_earth_r">gist_earth reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff
changeset
|
151 <option value="gist_yarg_r">gist_yarg reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
152 <option value="gist_ncar_r">gist_ncar reversed</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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changeset
|
153 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
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154 <option value="gist_heat_r">gist_heat reversed</option> |
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155 <option value="gnuplot_r">gnuplot reversed</option> |
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156 <option value="gnuplot2_r">gnuplot2 reversed</option> |
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157 <option value="CMRmap_r">CMRmap reversed</option> |
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158 <option value="bwr_r">bwr reversed</option> |
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159 <option value="hsv_r">hsv reversed</option> |
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160 <option value="brg_r">brg reversed</option> |
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161 <option value="jet_r">jet reversed</option> |
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162 <option value="afmhot_r">afmhot reversed</option> |
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163 </param> |
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164 </xml> |
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165 |
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166 |
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167 <xml name="multiple_input_matrices"> |
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168 <repeat name="input_files" title="HiC Matrix files" min="2"> |
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169 <param name="matrix" type="data" format="h5,cool" |
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170 label="HiC Matrix file" |
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171 help=""/> |
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172 <param name="mlabel" type="text" size="30" optional="true" value="" |
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173 label="Label" |
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174 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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175 </repeat> |
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176 </xml> |
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177 |
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178 <token name="@multiple_input_matrices@"> |
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179 #set $matrices = [] |
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180 #set $mlabels = [] |
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181 #for $counter, $i in enumerate($input_files): |
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182 ln -s $i.matrix #echo str($counter)+'_matrix'#; |
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183 #silent $matrices.append( '%s_matrix' % $counter ) |
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184 |
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185 #if str($i.mlabel.value) != "": |
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186 #set $mlabels += ['"%s"' % ($i.mlabel.value)] |
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187 #else |
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188 #set $mlabels += ['"%s"' % ($i.matrix.name)] |
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189 #end if |
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190 #end for |
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191 #set $mlabels = ' '.join($mlabels) |
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192 #set $matrices = ' '.join($matrices) |
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193 </token> |
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194 |
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195 |
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196 <xml name="region"> |
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197 <param name="region" type="text" label="Region of the genome to limit the operation" |
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198 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/> |
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199 </xml> |
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200 |
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201 |
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202 |
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203 <xml name="kmeans_clustering"> |
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204 <conditional name="used_multiple_regions"> |
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205 <param name="used_multiple_regions_options" type="select" |
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206 label="Did you compute the matrix with more than one groups of regions?" |
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207 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> |
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208 <option value="yes">Yes, I used multiple groups of regions</option> |
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209 <option value="no">No, I used only one group</option> |
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210 </param> |
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211 <when value="no"> |
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212 <conditional name="clustering"> |
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213 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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214 <option value="none">No clustering</option> |
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215 <option value="kmeans">Kmeans clustering</option> |
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216 </param> |
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217 <when value="kmeans"> |
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218 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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219 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/> |
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220 </when> |
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221 <when value="none" /> |
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222 </conditional> |
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223 </when> |
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224 <when value="yes" /> |
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225 </conditional> |
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226 </xml> |
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227 |
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228 <token name="@KMEANS_CLUSTERING@"> |
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229 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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230 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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231 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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232 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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233 #end if |
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234 #end if |
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235 #end if |
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236 </token> |
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237 |
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238 <xml name="samFlag"> |
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239 <param name="samFlag" type="integer" optional="true" value="" |
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240 label="Filter reads based on the SAM flag" |
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241 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/> |
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242 </xml> |
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243 <xml name="plotNumbers"> |
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244 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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245 label="Plot the correlation value" |
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246 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> |
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247 </xml> |
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248 <xml name="doNotExtendPairedEnds"> |
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249 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" |
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250 label="Do not extend paired ends" |
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251 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/> |
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252 </xml> |
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253 |
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254 <xml name="ignoreDuplicates"> |
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255 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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256 label="Ignore duplicates" |
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257 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" /> |
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258 </xml> |
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259 |
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260 <xml name="minMappingQuality"> |
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261 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" |
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262 label="Minimum mapping quality" |
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263 help= "If set, only reads that have a mapping quality score higher than the given value are considered. |
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264 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. |
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265 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> |
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266 </xml> |
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267 |
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268 <xml name="skipZeros"> |
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269 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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270 label ="Skip zeros" |
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271 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" /> |
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272 </xml> |
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273 |
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274 <xml name="fragmentLength"> |
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275 <param name="fragmentLength" type="integer" value="300" min="1" |
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276 label="Fragment length used for the sequencing" |
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277 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/> |
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278 </xml> |
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279 |
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280 <xml name="scaleFactor"> |
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281 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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282 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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283 </xml> |
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284 |
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285 <xml name="xMax"> |
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286 <param argument="--xMax" name="xMax" type="integer" optional="true" value="" |
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287 label="Max value for the x-axis in counts per bin" /> |
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288 </xml> |
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289 |
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290 <xml name="filterThreshold"> |
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291 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" |
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292 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/> |
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293 |
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294 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" |
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295 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/> |
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296 </xml> |
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297 |
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298 |
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299 <xml name="pseudocount"> |
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300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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301 </xml> |
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302 <xml name='matrix_h5_cooler_macro'> |
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303 <param name='matrix_h5_cooler' type="data" format="h5,cool" |
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304 label="Matrix to compute on."/> |
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305 |
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306 </xml> |
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307 <xml name='matrix_h5_cooler_multiple_macro'> |
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308 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" |
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309 label="Matrix to compute on." multiple="True"/> |
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310 </xml> |
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311 <token name="@REFERENCES@"> |
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312 |
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313 .. class:: infomark |
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314 |
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315 For more information on the tools, please visit our `help site`_. |
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316 |
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317 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com |
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318 |
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319 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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320 |
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321 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
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322 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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323 .. _help site: https://hicexplorer.readthedocs.org |
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324 |
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325 </token> |
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326 |
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327 |
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328 <xml name="multiple_input_bams"> |
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329 <repeat name="input_files" title="BAM files" min="2"> |
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330 <param name="bamfile" type="data" format="bam" |
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331 label="Bam file" |
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332 help="The BAM file must be sorted."/> |
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333 <param name="label" type="text" size="30" optional="true" value="" |
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334 label="Label" |
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335 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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336 </repeat> |
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337 </xml> |
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338 |
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339 <xml name="multiple_input_bigwigs"> |
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340 <repeat name="input_files" title="BigWig files" min="2"> |
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341 <param name="bigwigfile" type="data" format="bigwig" |
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342 label="Bigwig file" |
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343 help="The Bigwig file must be sorted."/> |
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344 <param name="label" type="text" size="30" optional="true" value="" |
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345 label="Label" |
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346 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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347 </repeat> |
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348 </xml> |
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349 |
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350 <xml name="plotTitle"> |
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351 <param name="plotTitle" type="text" value="" size="30" optional="True" |
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352 label="Title of the plot" |
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353 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
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354 </xml> |
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355 |
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356 <token name="@multiple_input_bams@"> |
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357 #import tempfile |
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358 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
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359 #set files=[] |
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360 #set labels=[] |
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361 #for $i in $input_files: |
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362 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
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363 #set $temp_input_path = $temp_input_handle.name |
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364 #silent $temp_input_handle.close() |
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365 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
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366 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
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367 #silent $files.append('%s.bam' % $temp_input_path) |
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368 |
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369 ##set $files += [str($i.bamfile)] |
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370 #if str($i.label.value) != "": |
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371 #set $labels += ["\"%s\"" % ($i.label.value)] |
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372 #else |
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373 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
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374 #end if |
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375 #end for |
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376 </token> |
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377 |
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378 <token name="@multiple_input_bigwigs@"> |
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379 #import tempfile |
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380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
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381 #set files=[] |
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382 #set labels=[] |
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383 #for $i in $input_files: |
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384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
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385 #set $temp_input_path = $temp_input_handle.name |
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386 #silent $temp_input_handle.close() |
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387 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
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388 #silent $files.append('%s.bw' % $temp_input_path) |
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389 |
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390 ##set $files += [str($i.bigwigfile)] |
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391 #if str($i.label.value) != "": |
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392 #set $labels += ["\"%s\"" % ($i.label.value)] |
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393 #else |
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394 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
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395 #end if |
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396 #end for |
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397 </token> |
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398 |
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399 <xml name="reference_genome_source"> |
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400 <conditional name="source"> |
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401 <param name="ref_source" type="select" label="Reference genome"> |
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402 <option value="cached">locally cached</option> |
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403 <option value="history">in your history</option> |
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404 </param> |
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405 <when value="cached"> |
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406 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
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407 <options from_data_table="deepTools_seqs"> |
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408 <filter type="sort_by" column="1" /> |
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409 <validator type="no_options" message="No indexes are available." /> |
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410 </options> |
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411 </param> |
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412 </when> |
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413 <when value="history"> |
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414 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
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415 </when> |
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416 </conditional> |
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417 </xml> |
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418 |
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419 <token name="@reference_genome_source@"> |
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420 #if $source.ref_source=="history": |
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421 --genome $source.input1 |
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422 #else: |
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423 --genome "${source.input1_2bit.fields.path}" |
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424 #end if |
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425 </token> |
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426 |
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427 <xml name="effectiveGenomeSize"> |
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428 <conditional name="effectiveGenomeSize"> |
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429 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
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430 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. |
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431 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
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432 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> |
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433 <option value="93260000">ce10 (93260000)</option> |
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434 <option value="121400000">dm3 (121400000)</option> |
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435 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
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436 <option value="2150570000">mm9 (2150570000)</option> |
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437 <option value="specific">user specified</option> |
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438 </param> |
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439 <when value="specific"> |
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440 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
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441 </when> |
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442 <when value="2150570000" /> |
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443 <when value="2451960000" /> |
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444 <when value="121400000" /> |
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445 <when value="93260000" /> |
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446 </conditional> |
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447 </xml> |
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448 |
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449 <xml name="image_file_format"> |
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450 <param name="outFileFormat" type="select" label="Image file format"> |
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451 <option value="png" selected="true">png</option> |
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452 <option value="pdf">pdf</option> |
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453 <option value="svg">svg</option> |
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454 <option value="eps">eps</option> |
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455 <option value="emf">emf</option> |
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456 </param> |
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457 </xml> |
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458 |
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459 <xml name="missingDataAsZero"> |
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460 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" |
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461 label ="Treat missing data as zero" |
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462 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." /> |
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463 </xml> |
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464 |
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465 <xml name="input_save_matrix_values"> |
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466 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
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467 </xml> |
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468 |
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469 <xml name="input_graphic_output_settings"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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470 <conditional name="output" > |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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471 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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472 <option value="no" selected="true">no</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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473 <option value="yes">yes</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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474 </param> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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475 <when value="no" /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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476 <when value="yes"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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477 <yield /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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478 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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479 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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480 </when> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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481 </conditional> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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482 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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483 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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484 <xml name="input_image_file_format"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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485 <param name="outFileFormat" type="select" label="Image file format"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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486 <option value="png" selected="true">png</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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487 <option value="pdf">pdf</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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488 <option value="svg">svg</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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489 <option value="eps">eps</option> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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490 <option value="emf">emf</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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491 </param> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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492 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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493 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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494 <xml name="output_image_file_format"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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495 <data format="png" name="outFileName" label="${tool.name} image"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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496 <change_format> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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497 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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498 <when input="output.outFileFormat" value="svg" format="svg" /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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499 <when input="output.outFileFormat" value="eps" format="eps" /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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500 <when input="output.outFileFormat" value="emf" format="emf" /> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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501 </change_format> |
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502 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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503 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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504 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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505 <xml name="output_save_matrix_values"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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506 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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507 <filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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508 (( |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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509 output['showOutputSettings'] == 'yes' and |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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510 output['saveMatrix'] is True |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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511 )) |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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512 </filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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513 </data> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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514 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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515 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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516 <xml name="output_graphic_outputs"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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517 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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518 <filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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519 (( |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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520 output['showOutputSettings'] == 'yes' and |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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521 output['saveData'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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522 )) |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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523 </filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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524 </data> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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525 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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526 <filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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527 (( |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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528 output['showOutputSettings'] == 'yes' and |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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529 output['saveSortedRegions'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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530 )) |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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531 </filter> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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532 </data> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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533 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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534 |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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535 <xml name="track_input_h5_macro"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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536 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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537 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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538 <xml name="track_input_bed_macro"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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539 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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540 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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541 <xml name="track_input_bedgraph_macro"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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542 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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543 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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544 <xml name="track_input_bigwig_macro"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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545 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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546 </xml> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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547 <xml name="track_input_bedgraph_matrix_macro"> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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548 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> |
61165fbb020d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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549 </xml> |
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550 <xml name="track_input_tabular_macro"> |
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551 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/> |
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552 </xml> |
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553 <xml name="plot_title"> |
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554 <param name="title" type="text" optional="true" label="Plot title"/> |
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555 </xml> |
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556 |
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557 <xml name="spacer_macro"> |
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558 <param name="spacer_width" type="float" value="" optional="True" |
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559 label="Include spacer at the end of the track." help="Width of the spacer." /> |
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560 </xml> |
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561 <xml name="fontsize_macro"> |
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562 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
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563 </xml> |
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564 </macros> |