Mercurial > repos > bgruening > hicexplorer_hicplotmatrix
annotate macros.xml @ 5:c3703afea1b1 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 09:21:50 -0500 |
parents | fd5e51d2b558 |
children | 268a01fbf402 |
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0
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <macros> |
2
2c0069f645bc
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
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c3703afea1b1
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> |
0
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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4 <xml name="requirements"> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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5 <requirements> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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7 <yield /> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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8 </requirements> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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9 <version_command>@BINARY@ --version</version_command> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 </xml> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 <xml name="citations"> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 <citations> |
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c3703afea1b1
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> |
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a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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15 <yield /> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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16 </citations> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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17 </xml> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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18 |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19 <xml name="zMax"> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 --> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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21 </xml> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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22 |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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23 <xml name="colormap"> |
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fd5e51d2b558
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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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"> |
0
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 <option value="RdYlBu">RdYlBu</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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26 <option value="Accent">Accent</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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27 <option value="Spectral">Spectral</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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28 <option value="Set1">Set1</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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29 <option value="Set2">Set2</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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30 <option value="Set3">Set3</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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31 <option value="Dark2">Dark2</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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32 <option value="Reds">Reds</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 <option value="Oranges">Oranges</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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34 <option value="Greens">Greens</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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35 <option value="Blues">Blues</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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36 <option value="Greys">Greys</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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37 <option value="Purples">Purples</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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38 <option value="Paired">Paired</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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39 <option value="Pastel1">Pastel1</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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40 <option value="Pastel2">Pastel2</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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41 <option value="spring">spring</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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42 <option value="summer">summer</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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43 <option value="autumn">autumn</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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44 <option value="winter">winter</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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45 <option value="hot">hot</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 <option value="coolwarm">coolwarm</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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47 <option value="cool">cool</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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48 <option value="seismic">seismic</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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49 <option value="terrain">terrain</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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50 <option value="ocean">ocean</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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51 <option value="rainbow">rainbow</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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52 <option value="bone">bone</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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55 <option value="cubehelix">cubehelix</option> |
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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57 <option value="pink">pink</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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62 <option value="BuPu">BuPu</option> |
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63 <option value="GnBu">GnBu</option> |
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64 <option value="OrRd">OrRd</option> |
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65 <option value="PiYG">PiYG</option> |
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66 <option value="PRGn">PRGn</option> |
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67 <option value="PuOr">PuOr</option> |
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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70 <option value="RdBu">RdBu</option> |
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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72 <option value="RdPu">RdPu</option> |
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73 <option value="YlGn">YlGn</option> |
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
77 <option value="YlOrBr">YlOrBr</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
78 <option value="YlOrRd">YlOrRd</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
79 <option value="gist_gray">gist_gray</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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changeset
|
80 <option value="gist_stern">gist_stern</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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changeset
|
81 <option value="gist_earth">gist_earth</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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changeset
|
82 <option value="gist_yarg">gist_yarg</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
83 <option value="gist_ncar">gist_ncar</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
84 <option value="gist_rainbow">gist_rainbow</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
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changeset
|
85 <option value="gist_heat">gist_heat</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
86 <option value="gnuplot">gnuplot</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
87 <option value="gnuplot2">gnuplot2</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
88 <option value="CMRmap">CMRmap</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
89 <option value="bwr">bwr</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
90 <option value="hsv">hsv</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
91 <option value="brg">brg</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
92 <option value="jet">jet</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
93 <option value="afmhot">afmhot</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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changeset
|
94 <option value="Accent_r">Accent reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
95 <option value="Spectral_r">Spectral reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
96 <option value="Set1_r">Set1 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
97 <option value="Set2_r">Set2 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
98 <option value="Set3_r">Set3 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
99 <option value="Dark2_r">Dark2 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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100 <option value="Reds_r">Reds reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
101 <option value="Oranges_r">Oranges reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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102 <option value="Greens_r">Greens reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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103 <option value="Blues_r">Blues reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
104 <option value="Greys_r">Greys reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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105 <option value="Purples_r">Purples reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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106 <option value="Paired_r">Paired reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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107 <option value="Pastel1_r">Pastel1 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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108 <option value="Pastel2_r">Pastel2 reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
109 <option value="spring_r">spring reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
110 <option value="summer_r">summer reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
111 <option value="autumn_r">autumn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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112 <option value="winter_r">winter reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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113 <option value="hot_r">hot reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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114 <option value="coolwarm_r">coolwarm reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
115 <option value="cool_r">cool reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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116 <option value="seismic_r">seismic reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
117 <option value="terrain_r">terrain reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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118 <option value="ocean_r">ocean reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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119 <option value="rainbow_r">rainbow reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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120 <option value="bone_r">bone reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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121 <option value="flag_r">flag reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
122 <option value="prism_r">prism reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
123 <option value="cubehelix_r">cubehelix reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
124 <option value="binary_r">binary reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
125 <option value="pink_r">pink reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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126 <option value="gray_r">gray reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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127 <option value="copper_r">copper reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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128 <option value="BrBG_r">BrBG reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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129 <option value="BuGn_r">BuGn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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130 <option value="BuPu_r">BuPu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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131 <option value="GnBu_r">GnBu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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132 <option value="OrRd_r">OrRd reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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133 <option value="PiYG_r">PiYG reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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134 <option value="PRGn_r">PRGn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
135 <option value="PuOr_r">PuOr reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
136 <option value="PuRd_r">PuRd reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
137 <option value="PuBu_r">PuBu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
138 <option value="RdBu_r">RdBu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
139 <option value="RdGy_r">RdGy reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
140 <option value="RdPu_r">RdPu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
141 <option value="YlGn_r">YlGn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
142 <option value="PuBuGn_r">PuBuGn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
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|
143 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
144 <option value="RdYlGn_r">RdYlGn reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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changeset
|
145 <option value="YlGnBu_r">YlGnBu reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
146 <option value="YlOrBr_r">YlOrBr reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
147 <option value="YlOrRd_r">YlOrRd reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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|
148 <option value="gist_gray_r">gist_gray reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
149 <option value="gist_stern_r">gist_stern reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
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|
150 <option value="gist_earth_r">gist_earth reversed</option> |
a9050bffb50c
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
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changeset
|
151 <option value="gist_yarg_r">gist_yarg reversed</option> |
a9050bffb50c
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152 <option value="gist_ncar_r">gist_ncar reversed</option> |
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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> |
0
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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467 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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468 |
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469 <xml name="input_graphic_output_settings"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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470 <conditional name="output" > |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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471 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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472 <option value="no" selected="true">no</option> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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473 <option value="yes">yes</option> |
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474 </param> |
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475 <when value="no" /> |
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476 <when value="yes"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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477 <yield /> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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478 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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."/> |
a9050bffb50c
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480 </when> |
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481 </conditional> |
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482 </xml> |
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483 |
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484 <xml name="input_image_file_format"> |
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485 <param name="outFileFormat" type="select" label="Image file format"> |
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486 <option value="png" selected="true">png</option> |
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487 <option value="pdf">pdf</option> |
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488 <option value="svg">svg</option> |
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489 <option value="eps">eps</option> |
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490 <option value="emf">emf</option> |
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491 </param> |
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492 </xml> |
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493 |
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494 <xml name="output_image_file_format"> |
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495 <data format="png" name="outFileName" label="${tool.name} image"> |
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496 <change_format> |
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497 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
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498 <when input="output.outFileFormat" value="svg" format="svg" /> |
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499 <when input="output.outFileFormat" value="eps" format="eps" /> |
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500 <when input="output.outFileFormat" value="emf" format="emf" /> |
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501 </change_format> |
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502 </data> |
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503 </xml> |
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504 |
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505 <xml name="output_save_matrix_values"> |
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506 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
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507 <filter> |
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508 (( |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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509 output['showOutputSettings'] == 'yes' and |
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510 output['saveMatrix'] is True |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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511 )) |
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512 </filter> |
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513 </data> |
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514 </xml> |
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515 |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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516 <xml name="output_graphic_outputs"> |
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517 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
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518 <filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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519 (( |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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520 output['showOutputSettings'] == 'yes' and |
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521 output['saveData'] is True |
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522 )) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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523 </filter> |
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524 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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525 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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526 <filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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527 (( |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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528 output['showOutputSettings'] == 'yes' and |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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530 )) |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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531 </filter> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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532 </data> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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533 </xml> |
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534 |
2
2c0069f645bc
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535 <xml name="track_input_h5_macro"> |
5
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536 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> |
2
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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537 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538 <xml name="track_input_bed_macro"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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539 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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540 </xml> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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541 <xml name="track_input_bedgraph_macro"> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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542 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> |
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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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543 </xml> |
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544 <xml name="track_input_bigwig_macro"> |
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545 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/> |
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546 </xml> |
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547 <xml name="track_input_bedgraph_matrix_macro"> |
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548 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> |
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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 |
2
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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> |