Mercurial > repos > bgruening > hicexplorer_hicpca
annotate macros.xml.orig @ 3:ea50f7bba657 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author | iuc |
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date | Wed, 07 Mar 2018 03:26:15 -0500 |
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3
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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1 <macros> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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3 <<<<<<< HEAD |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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4 <token name="@WRAPPER_VERSION@">2.0</token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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5 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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6 <token name="@USE_RANGE@"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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7 #if $use_range.select_use_range == "yes_use_range": |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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8 --range $range_min:$range_max |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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9 #end if |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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10 </token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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11 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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12 ======= |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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13 <token name="@WRAPPER_VERSION@">2.1alpha1</token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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14 >>>>>>> joachimwolff-master |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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15 <xml name="requirements"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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16 <requirements> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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18 <yield /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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19 </requirements> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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20 <version_command>@BINARY@ --version</version_command> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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21 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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22 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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23 <xml name="citations"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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24 <citations> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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25 <citation type="doi">10.5281/zenodo.1133705</citation> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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26 <yield /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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27 </citations> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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28 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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29 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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30 <xml name="zMax"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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31 <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 --> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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32 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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33 <xml name="use_range"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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35 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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36 <option value="no_use_range">No restriction</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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37 <option value="yes_use_range">Only consider counts within a range</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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38 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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39 <when value="no_use_range"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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40 <when value="yes_use_range"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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41 <param name="range_min" type="integer" value="" min="0"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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42 <param name="range_max" type="integer" value="" min="0"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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43 </when> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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44 </conditional> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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45 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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46 <xml name="colormap"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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47 <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"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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48 <option value="RdYlBu">RdYlBu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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49 <option value="Accent">Accent</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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50 <option value="Spectral">Spectral</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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51 <option value="Set1">Set1</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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52 <option value="Set2">Set2</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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53 <option value="Set3">Set3</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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54 <option value="Dark2">Dark2</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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55 <option value="Reds">Reds</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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56 <option value="Oranges">Oranges</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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57 <option value="Greens">Greens</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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58 <option value="Blues">Blues</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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59 <option value="Greys">Greys</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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60 <option value="Purples">Purples</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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61 <option value="Paired">Paired</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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62 <option value="Pastel1">Pastel1</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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63 <option value="Pastel2">Pastel2</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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64 <option value="spring">spring</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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65 <option value="summer">summer</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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66 <option value="autumn">autumn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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67 <option value="winter">winter</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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68 <option value="hot">hot</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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69 <option value="coolwarm">coolwarm</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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70 <option value="cool">cool</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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71 <option value="seismic">seismic</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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72 <option value="terrain">terrain</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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73 <option value="ocean">ocean</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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74 <option value="rainbow">rainbow</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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75 <option value="bone">bone</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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76 <option value="flag">flag</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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77 <option value="prism">prism</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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78 <option value="cubehelix">cubehelix</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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79 <option value="binary">binary</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
80 <option value="pink">pink</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
81 <option value="gray">gray</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
82 <option value="copper">copper</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
83 <option value="BrBG">BrBG</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
84 <option value="BuGn">BuGn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
85 <option value="BuPu">BuPu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
86 <option value="GnBu">GnBu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
87 <option value="OrRd">OrRd</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
88 <option value="PiYG">PiYG</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
89 <option value="PRGn">PRGn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
90 <option value="PuOr">PuOr</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
91 <option value="PuRd">PuRd</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
92 <option value="PuBu">PuBu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
93 <option value="RdBu">RdBu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
94 <option value="RdGy">RdGy</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
95 <option value="RdPu">RdPu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
96 <option value="YlGn">YlGn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
97 <option value="PuBuGn">PuBuGn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
98 <option value="RdYlGn">RdYlGn</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
99 <option value="YlGnBu">YlGnBu</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
100 <option value="YlOrBr">YlOrBr</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
101 <option value="YlOrRd">YlOrRd</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
102 <option value="gist_gray">gist_gray</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
103 <option value="gist_stern">gist_stern</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
104 <option value="gist_earth">gist_earth</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
105 <option value="gist_yarg">gist_yarg</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
106 <option value="gist_ncar">gist_ncar</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
107 <option value="gist_rainbow">gist_rainbow</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
108 <option value="gist_heat">gist_heat</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
109 <option value="gnuplot">gnuplot</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
110 <option value="gnuplot2">gnuplot2</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
111 <option value="CMRmap">CMRmap</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
112 <option value="bwr">bwr</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
113 <option value="hsv">hsv</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
114 <option value="brg">brg</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
115 <option value="jet">jet</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
116 <option value="afmhot">afmhot</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
117 <option value="Accent_r">Accent reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
118 <option value="Spectral_r">Spectral reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
119 <option value="Set1_r">Set1 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
120 <option value="Set2_r">Set2 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
121 <option value="Set3_r">Set3 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
122 <option value="Dark2_r">Dark2 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
123 <option value="Reds_r">Reds reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
124 <option value="Oranges_r">Oranges reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
125 <option value="Greens_r">Greens reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
126 <option value="Blues_r">Blues reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
127 <option value="Greys_r">Greys reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
128 <option value="Purples_r">Purples reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
129 <option value="Paired_r">Paired reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
130 <option value="Pastel1_r">Pastel1 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
131 <option value="Pastel2_r">Pastel2 reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
132 <option value="spring_r">spring reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
133 <option value="summer_r">summer reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
134 <option value="autumn_r">autumn reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
135 <option value="winter_r">winter reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
136 <option value="hot_r">hot reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
137 <option value="coolwarm_r">coolwarm reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
138 <option value="cool_r">cool reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
139 <option value="seismic_r">seismic reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
140 <option value="terrain_r">terrain reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
141 <option value="ocean_r">ocean reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
142 <option value="rainbow_r">rainbow reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
143 <option value="bone_r">bone reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
144 <option value="flag_r">flag reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
145 <option value="prism_r">prism reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
146 <option value="cubehelix_r">cubehelix reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
147 <option value="binary_r">binary reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
148 <option value="pink_r">pink reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
149 <option value="gray_r">gray reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
150 <option value="copper_r">copper reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
151 <option value="BrBG_r">BrBG reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
152 <option value="BuGn_r">BuGn reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
153 <option value="BuPu_r">BuPu reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
154 <option value="GnBu_r">GnBu reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
155 <option value="OrRd_r">OrRd reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
156 <option value="PiYG_r">PiYG reversed</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
157 <option value="PRGn_r">PRGn reversed</option> |
ea50f7bba657
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158 <option value="PuOr_r">PuOr reversed</option> |
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159 <option value="PuRd_r">PuRd reversed</option> |
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160 <option value="PuBu_r">PuBu reversed</option> |
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161 <option value="RdBu_r">RdBu reversed</option> |
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162 <option value="RdGy_r">RdGy reversed</option> |
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163 <option value="RdPu_r">RdPu reversed</option> |
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164 <option value="YlGn_r">YlGn reversed</option> |
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165 <option value="PuBuGn_r">PuBuGn reversed</option> |
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166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> |
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167 <option value="RdYlGn_r">RdYlGn reversed</option> |
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168 <option value="YlGnBu_r">YlGnBu reversed</option> |
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169 <option value="YlOrBr_r">YlOrBr reversed</option> |
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170 <option value="YlOrRd_r">YlOrRd reversed</option> |
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171 <option value="gist_gray_r">gist_gray reversed</option> |
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172 <option value="gist_stern_r">gist_stern reversed</option> |
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173 <option value="gist_earth_r">gist_earth reversed</option> |
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174 <option value="gist_yarg_r">gist_yarg reversed</option> |
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175 <option value="gist_ncar_r">gist_ncar reversed</option> |
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176 <option value="gist_rainbow_r">gist_rainbow reversed</option> |
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177 <option value="gist_heat_r">gist_heat reversed</option> |
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178 <option value="gnuplot_r">gnuplot reversed</option> |
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179 <option value="gnuplot2_r">gnuplot2 reversed</option> |
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180 <option value="CMRmap_r">CMRmap reversed</option> |
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181 <option value="bwr_r">bwr reversed</option> |
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182 <option value="hsv_r">hsv reversed</option> |
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183 <option value="brg_r">brg reversed</option> |
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184 <option value="jet_r">jet reversed</option> |
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185 <option value="afmhot_r">afmhot reversed</option> |
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186 </param> |
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187 </xml> |
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188 |
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189 |
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190 <xml name="multiple_input_matrices"> |
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191 <repeat name="input_files" title="HiC Matrix files" min="2"> |
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192 <param name="matrix" type="data" format="h5,cool" |
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193 label="HiC Matrix file" |
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194 help=""/> |
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195 <param name="mlabel" type="text" size="30" optional="true" value="" |
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196 label="Label" |
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197 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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198 </repeat> |
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199 </xml> |
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200 |
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201 <token name="@multiple_input_matrices@"> |
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202 #set $matrices = [] |
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203 #set $mlabels = [] |
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204 #for $counter, $i in enumerate($input_files): |
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205 ln -s $i.matrix #echo str($counter)+'_matrix'#; |
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206 #silent $matrices.append( '%s_matrix' % $counter ) |
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207 |
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208 #if str($i.mlabel.value) != "": |
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209 #set $mlabels += ['"%s"' % ($i.mlabel.value)] |
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210 #else |
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211 #set $mlabels += ['"%s"' % ($i.matrix.name)] |
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212 #end if |
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213 #end for |
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214 #set $mlabels = ' '.join($mlabels) |
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215 #set $matrices = ' '.join($matrices) |
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216 </token> |
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217 |
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218 |
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219 <xml name="region"> |
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220 <param name="region" type="text" label="Region of the genome to limit the operation" |
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221 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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222 </xml> |
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223 |
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224 |
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225 |
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226 <xml name="kmeans_clustering"> |
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227 <conditional name="used_multiple_regions"> |
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228 <param name="used_multiple_regions_options" type="select" |
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229 label="Did you compute the matrix with more than one groups of regions?" |
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230 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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231 <option value="yes">Yes, I used multiple groups of regions</option> |
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232 <option value="no">No, I used only one group</option> |
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233 </param> |
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234 <when value="no"> |
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235 <conditional name="clustering"> |
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236 <param name="clustering_options" type="select" label="Clustering algorithm"> |
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237 <option value="none">No clustering</option> |
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238 <option value="kmeans">Kmeans clustering</option> |
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239 </param> |
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240 <when value="kmeans"> |
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241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" |
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242 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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243 </when> |
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244 <when value="none" /> |
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245 </conditional> |
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246 </when> |
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247 <when value="yes" /> |
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248 </conditional> |
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249 </xml> |
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250 |
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251 <token name="@KMEANS_CLUSTERING@"> |
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252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': |
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253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': |
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254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: |
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255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans |
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256 #end if |
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257 #end if |
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258 #end if |
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259 </token> |
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260 |
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261 <xml name="samFlag"> |
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262 <param name="samFlag" type="integer" optional="true" value="" |
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263 label="Filter reads based on the SAM flag" |
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264 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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265 </xml> |
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266 <xml name="plotNumbers"> |
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267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" |
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268 label="Plot the correlation value" |
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269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/> |
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270 </xml> |
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271 <xml name="doNotExtendPairedEnds"> |
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272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" |
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273 label="Do not extend paired ends" |
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274 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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275 </xml> |
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276 |
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277 <xml name="ignoreDuplicates"> |
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278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" |
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279 label="Ignore duplicates" |
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280 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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281 </xml> |
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282 |
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283 <xml name="minMappingQuality"> |
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284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1" |
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285 label="Minimum mapping quality" |
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286 help= "If set, only reads that have a mapping quality score higher than the given value are considered. |
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287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. |
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288 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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289 </xml> |
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290 |
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291 <xml name="skipZeros"> |
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292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
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293 label ="Skip zeros" |
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294 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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295 </xml> |
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296 |
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297 <xml name="fragmentLength"> |
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298 <param name="fragmentLength" type="integer" value="300" min="1" |
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299 label="Fragment length used for the sequencing" |
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300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/> |
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301 </xml> |
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302 |
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303 <xml name="scaleFactor"> |
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304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> |
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305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> |
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306 </xml> |
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307 |
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308 <xml name="xMax"> |
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309 <param argument="--xMax" name="xMax" type="integer" optional="true" value="" |
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310 label="Max value for the x-axis in counts per bin" /> |
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311 </xml> |
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312 |
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313 <xml name="filterThreshold"> |
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314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" |
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315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/> |
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316 |
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317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0" |
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318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/> |
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319 </xml> |
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320 |
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321 <xml name="pseudocount"> |
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322 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> |
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323 </xml> |
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324 <xml name='matrix_h5_cooler_macro'> |
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325 <param name='matrix_h5_cooler' type="data" format="h5,cool" |
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326 label="Matrix to compute on"/> |
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327 </xml> |
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328 <xml name='matrix_h5_cooler_multiple_macro'> |
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329 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" |
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330 label="Matricies to compute on" multiple="true"/> |
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331 </xml> |
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332 <token name="@REFERENCES@"> |
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333 |
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334 .. class:: infomark |
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335 |
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336 For more information on the tools, please visit our `help site`_. |
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337 |
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338 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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339 |
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340 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. |
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341 |
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342 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ |
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343 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de |
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344 .. _help site: https://hicexplorer.readthedocs.org |
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345 |
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346 </token> |
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347 |
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348 |
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349 <xml name="multiple_input_bams"> |
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350 <repeat name="input_files" title="BAM files" min="2"> |
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351 <param name="bamfile" type="data" format="bam" |
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352 label="Bam file" |
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353 help="The BAM file must be sorted."/> |
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354 <param name="label" type="text" size="30" optional="true" value="" |
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355 label="Label" |
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356 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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357 </repeat> |
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358 </xml> |
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359 |
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360 <xml name="multiple_input_bigwigs"> |
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361 <repeat name="input_files" title="BigWig files" min="2"> |
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362 <param name="bigwigfile" type="data" format="bigwig" |
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363 label="Bigwig file" |
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364 help="The Bigwig file must be sorted."/> |
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365 <param name="label" type="text" size="30" optional="true" value="" |
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366 label="Label" |
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367 help="Label to use in the output. If not given the dataset name will be used instead."/> |
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368 </repeat> |
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369 </xml> |
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370 |
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371 <xml name="plotTitle"> |
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372 <param name="plotTitle" type="text" value="" size="30" optional="True" |
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373 label="Title of the plot" |
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374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" /> |
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375 </xml> |
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376 |
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377 <token name="@multiple_input_bams@"> |
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378 #import tempfile |
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379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
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380 #set files=[] |
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381 #set labels=[] |
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382 #for $i in $input_files: |
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383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
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384 #set $temp_input_path = $temp_input_handle.name |
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385 #silent $temp_input_handle.close() |
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386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) |
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387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) |
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388 #silent $files.append('%s.bam' % $temp_input_path) |
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389 |
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390 ##set $files += [str($i.bamfile)] |
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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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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
394 #set $labels += ["\"%s\"" % ($i.bamfile.name)] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
395 #end if |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
396 #end for |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
397 </token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
398 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
399 <token name="@multiple_input_bigwigs@"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
400 #import tempfile |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
402 #set files=[] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
403 #set labels=[] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
404 #for $i in $input_files: |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
406 #set $temp_input_path = $temp_input_handle.name |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
407 #silent $temp_input_handle.close() |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
409 #silent $files.append('%s.bw' % $temp_input_path) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
410 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
411 ##set $files += [str($i.bigwigfile)] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
412 #if str($i.label.value) != "": |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
413 #set $labels += ["\"%s\"" % ($i.label.value)] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
414 #else |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
416 #end if |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
417 #end for |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
418 </token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
419 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
420 <xml name="reference_genome_source"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
421 <conditional name="source"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
422 <param name="ref_source" type="select" label="Reference genome"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
423 <option value="cached">locally cached</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
424 <option value="history">in your history</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
425 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
426 <when value="cached"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
427 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
428 <options from_data_table="deepTools_seqs"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
429 <filter type="sort_by" column="1" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
430 <validator type="no_options" message="No indexes are available." /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
431 </options> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
432 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
433 </when> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
434 <when value="history"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
436 </when> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
437 </conditional> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
438 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
439 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
440 <token name="@reference_genome_source@"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
441 #if $source.ref_source=="history": |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
442 --genome $source.input1 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
443 #else: |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
444 --genome "${source.input1_2bit.fields.path}" |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
445 #end if |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
446 </token> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
447 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
448 <xml name="effectiveGenomeSize"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
449 <conditional name="effectiveGenomeSize"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
451 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. |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
453 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."> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
454 <option value="93260000">ce10 (93260000)</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
455 <option value="121400000">dm3 (121400000)</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
456 <option value="2451960000" selected="true">hg19 (2451960000)</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
457 <option value="2150570000">mm9 (2150570000)</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
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458 <option value="specific">user specified</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
459 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
460 <when value="specific"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
462 </when> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
463 <when value="2150570000" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
464 <when value="2451960000" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
465 <when value="121400000" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
466 <when value="93260000" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
467 </conditional> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
468 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
469 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
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470 <xml name="image_file_format"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
471 <param name="outFileFormat" type="select" label="Image file format"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
472 <option value="png" selected="true">png</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
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473 <option value="pdf">pdf</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
474 <option value="svg">svg</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
475 <option value="eps">eps</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
476 <option value="emf">emf</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
477 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
478 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
479 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
480 <xml name="missingDataAsZero"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
482 label ="Treat missing data as zero" |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
483 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." /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
484 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
485 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
486 <xml name="input_save_matrix_values"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
488 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
489 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
490 <xml name="input_graphic_output_settings"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
491 <conditional name="output" > |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
492 <param name="showOutputSettings" type="select" label="Show advanced output settings" > |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
493 <option value="no" selected="true">no</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
494 <option value="yes">yes</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
495 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
496 <when value="no" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
497 <when value="yes"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
498 <yield /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
500 <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."/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
501 </when> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
502 </conditional> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
503 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
504 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
505 <xml name="input_image_file_format"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
506 <param name="outFileFormat" type="select" label="Image file format"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
507 <option value="png" selected="true">png</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
508 <option value="pdf">pdf</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
509 <option value="svg">svg</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
510 <option value="eps">eps</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
511 <option value="emf">emf</option> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
512 </param> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
513 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
514 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
515 <xml name="output_image_file_format"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
516 <data format="png" name="outFileName" label="${tool.name} image"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
517 <change_format> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
518 <when input="output.outFileFormat" value="pdf" format="pdf" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
519 <when input="output.outFileFormat" value="svg" format="svg" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
520 <when input="output.outFileFormat" value="eps" format="eps" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
521 <when input="output.outFileFormat" value="emf" format="emf" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
522 </change_format> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
523 </data> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
524 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
525 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
526 <xml name="output_save_matrix_values"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
527 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
528 <filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
529 (( |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
530 output['showOutputSettings'] == 'yes' and |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
531 output['saveMatrix'] is True |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
532 )) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
533 </filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
534 </data> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
535 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
536 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
537 <xml name="output_graphic_outputs"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
538 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
539 <filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
540 (( |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
541 output['showOutputSettings'] == 'yes' and |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
542 output['saveData'] is True |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
543 )) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
544 </filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
545 </data> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
547 <filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
548 (( |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
549 output['showOutputSettings'] == 'yes' and |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
550 output['saveSortedRegions'] is True |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
551 )) |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
552 </filter> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
553 </data> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
554 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
|
555 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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556 <xml name="track_input_h5_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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557 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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558 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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559 <xml name="track_input_bed_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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diff
changeset
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560 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
changeset
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561 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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562 <xml name="track_input_bedgraph_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
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563 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
diff
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564 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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565 <xml name="track_input_bigwig_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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566 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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567 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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568 <xml name="track_input_bedgraph_matrix_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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569 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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570 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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571 <xml name="track_input_tabular_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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572 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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573 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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574 <xml name="plot_title"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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575 <param name="title" type="text" optional="true" label="Plot title"/> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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576 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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577 |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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578 <xml name="spacer_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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579 <param name="spacer_width" type="float" value="" optional="True" |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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580 label="Include spacer at the end of the track." help="Width of the spacer." /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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581 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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582 <xml name="fontsize_macro"> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents:
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583 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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584 </xml> |
ea50f7bba657
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
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585 </macros> |