Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate macros.xml @ 9:0399cd2c25aa draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:31:58 -0400
parents c109622e0cf5
children 6d1526527417
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <macros>
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2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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0399cd2c25aa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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3 <token name="@WRAPPER_VERSION@">2.1.2</token>
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iuc
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4 <token name="@USE_RANGE@">
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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5 #if $use_range.select_use_range == "yes_use_range":
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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6 --range $range_min:$range_max
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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7 #end if
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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8 </token>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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9
0
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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10 <xml name="requirements">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 <requirements>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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13 <yield />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 </requirements>
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15 <version_command>@BINARY@ --version</version_command>
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16 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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18 <xml name="citations">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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19 <citations>
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34da5ed2507c planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
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20 <citation type="doi">10.5281/zenodo.1133705</citation>
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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21 <yield />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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22 </citations>
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23 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 <xml name="zMax">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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26 <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 -->
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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27 </xml>
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28 <xml name="use_range">
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
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c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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31 <option value="no_use_range">No restriction</option>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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32 <option value="yes_use_range">Only consider counts within a range</option>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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33 </param>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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34 <when value="no_use_range"/>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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35 <when value="yes_use_range">
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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36 <expand macro='range' />
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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37 </when>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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38 </conditional>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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39 </xml>
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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41 <xml name="range">
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42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
0399cd2c25aa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
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43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
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44 </xml>
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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46 <xml name="colormap">
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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">
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c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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48 <option value="RdYlBu">RdYlBu</option>
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49 <option value="Accent">Accent</option>
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50 <option value="Spectral">Spectral</option>
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51 <option value="Set1">Set1</option>
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52 <option value="Set2">Set2</option>
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53 <option value="Set3">Set3</option>
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54 <option value="Dark2">Dark2</option>
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55 <option value="Reds">Reds</option>
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56 <option value="Oranges">Oranges</option>
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57 <option value="Greens">Greens</option>
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58 <option value="Blues">Blues</option>
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59 <option value="Greys">Greys</option>
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60 <option value="Purples">Purples</option>
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61 <option value="Paired">Paired</option>
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62 <option value="Pastel1">Pastel1</option>
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63 <option value="Pastel2">Pastel2</option>
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64 <option value="spring">spring</option>
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65 <option value="summer">summer</option>
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66 <option value="autumn">autumn</option>
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67 <option value="winter">winter</option>
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68 <option value="hot">hot</option>
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69 <option value="coolwarm">coolwarm</option>
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70 <option value="cool">cool</option>
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71 <option value="seismic">seismic</option>
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72 <option value="terrain">terrain</option>
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73 <option value="ocean">ocean</option>
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74 <option value="rainbow">rainbow</option>
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75 <option value="bone">bone</option>
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76 <option value="flag">flag</option>
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77 <option value="prism">prism</option>
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78 <option value="cubehelix">cubehelix</option>
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79 <option value="binary">binary</option>
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80 <option value="pink">pink</option>
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81 <option value="gray">gray</option>
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82 <option value="copper">copper</option>
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83 <option value="BrBG">BrBG</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
84 <option value="BuGn">BuGn</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
85 <option value="BuPu">BuPu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
86 <option value="GnBu">GnBu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
87 <option value="OrRd">OrRd</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
88 <option value="PiYG">PiYG</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
89 <option value="PRGn">PRGn</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
90 <option value="PuOr">PuOr</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
91 <option value="PuRd">PuRd</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
92 <option value="PuBu">PuBu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
93 <option value="RdBu">RdBu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
94 <option value="RdGy">RdGy</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
95 <option value="RdPu">RdPu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
96 <option value="YlGn">YlGn</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
97 <option value="PuBuGn">PuBuGn</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
98 <option value="RdYlGn">RdYlGn</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
99 <option value="YlGnBu">YlGnBu</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
100 <option value="YlOrBr">YlOrBr</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
101 <option value="YlOrRd">YlOrRd</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
102 <option value="gist_gray">gist_gray</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
103 <option value="gist_stern">gist_stern</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
104 <option value="gist_earth">gist_earth</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
105 <option value="gist_yarg">gist_yarg</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
106 <option value="gist_ncar">gist_ncar</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
107 <option value="gist_rainbow">gist_rainbow</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
108 <option value="gist_heat">gist_heat</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
109 <option value="gnuplot">gnuplot</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
110 <option value="gnuplot2">gnuplot2</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
111 <option value="CMRmap">CMRmap</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
112 <option value="bwr">bwr</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
113 <option value="hsv">hsv</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
114 <option value="brg">brg</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
115 <option value="jet">jet</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
116 <option value="afmhot">afmhot</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
117 <option value="Accent_r">Accent reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
118 <option value="Spectral_r">Spectral reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
119 <option value="Set1_r">Set1 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
120 <option value="Set2_r">Set2 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
121 <option value="Set3_r">Set3 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
122 <option value="Dark2_r">Dark2 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
123 <option value="Reds_r">Reds reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
124 <option value="Oranges_r">Oranges reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
125 <option value="Greens_r">Greens reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
126 <option value="Blues_r">Blues reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
127 <option value="Greys_r">Greys reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
128 <option value="Purples_r">Purples reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
129 <option value="Paired_r">Paired reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
130 <option value="Pastel1_r">Pastel1 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
131 <option value="Pastel2_r">Pastel2 reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
132 <option value="spring_r">spring reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
133 <option value="summer_r">summer reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
134 <option value="autumn_r">autumn reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
135 <option value="winter_r">winter reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
136 <option value="hot_r">hot reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
137 <option value="coolwarm_r">coolwarm reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
138 <option value="cool_r">cool reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
139 <option value="seismic_r">seismic reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
140 <option value="terrain_r">terrain reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
141 <option value="ocean_r">ocean reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
142 <option value="rainbow_r">rainbow reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
143 <option value="bone_r">bone reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
144 <option value="flag_r">flag reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
145 <option value="prism_r">prism reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
146 <option value="cubehelix_r">cubehelix reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
147 <option value="binary_r">binary reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
148 <option value="pink_r">pink reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
149 <option value="gray_r">gray reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
150 <option value="copper_r">copper reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
151 <option value="BrBG_r">BrBG reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
152 <option value="BuGn_r">BuGn reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
153 <option value="BuPu_r">BuPu reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
154 <option value="GnBu_r">GnBu reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
155 <option value="OrRd_r">OrRd reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
156 <option value="PiYG_r">PiYG reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
157 <option value="PRGn_r">PRGn reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
158 <option value="PuOr_r">PuOr reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
159 <option value="PuRd_r">PuRd reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
160 <option value="PuBu_r">PuBu reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
161 <option value="RdBu_r">RdBu reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
162 <option value="RdGy_r">RdGy reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
163 <option value="RdPu_r">RdPu reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
164 <option value="YlGn_r">YlGn reversed</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
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="Hi-C Matrix files" min="2">
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192 <param name="matrix" type="data" format="h5,cool"
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193 label="Hi-C 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)."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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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
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322 <xml name="pseudocount">
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323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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324 </xml>
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325 <xml name='matrix_h5_cooler_macro'>
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326 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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327 label="Matrix to compute on"/>
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328 </xml>
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329 <xml name='matrix_h5_cooler_multiple_macro'>
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330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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331 label="Matricies to compute on" multiple="true"/>
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332 </xml>
0
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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333 <token name="@REFERENCES@">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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334
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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335 .. class:: infomark
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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336
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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337 For more information on the tools, please visit our `help site`_.
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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338
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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339 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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340
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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341 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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342
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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345 .. _help site: https://hicexplorer.readthedocs.org
0
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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346
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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347 </token>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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348
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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349
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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350 <xml name="multiple_input_bams">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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351 <repeat name="input_files" title="BAM files" min="2">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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352 <param name="bamfile" type="data" format="bam"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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353 label="Bam file"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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354 help="The BAM file must be sorted."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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355 <param name="label" type="text" size="30" optional="true" value=""
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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356 label="Label"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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357 help="Label to use in the output. If not given the dataset name will be used instead."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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358 </repeat>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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359 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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360
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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361 <xml name="multiple_input_bigwigs">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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362 <repeat name="input_files" title="BigWig files" min="2">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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363 <param name="bigwigfile" type="data" format="bigwig"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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364 label="Bigwig file"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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365 help="The Bigwig file must be sorted."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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366 <param name="label" type="text" size="30" optional="true" value=""
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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367 label="Label"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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368 help="Label to use in the output. If not given the dataset name will be used instead."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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369 </repeat>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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370 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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371
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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372 <xml name="plotTitle">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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373 <param name="plotTitle" type="text" value="" size="30" optional="True"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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374 label="Title of the plot"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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376 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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377
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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378 <token name="@multiple_input_bams@">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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379 #import tempfile
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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381 #set files=[]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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382 #set labels=[]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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383 #for $i in $input_files:
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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385 #set $temp_input_path = $temp_input_handle.name
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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386 #silent $temp_input_handle.close()
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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389 #silent $files.append('%s.bam' % $temp_input_path)
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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390
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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391 ##set $files += [str($i.bamfile)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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392 #if str($i.label.value) != "":
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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393 #set $labels += ["\"%s\"" % ($i.label.value)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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394 #else
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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396 #end if
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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397 #end for
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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398 </token>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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399
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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400 <token name="@multiple_input_bigwigs@">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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401 #import tempfile
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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403 #set files=[]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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404 #set labels=[]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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405 #for $i in $input_files:
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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407 #set $temp_input_path = $temp_input_handle.name
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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408 #silent $temp_input_handle.close()
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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410 #silent $files.append('%s.bw' % $temp_input_path)
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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411
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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412 ##set $files += [str($i.bigwigfile)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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413 #if str($i.label.value) != "":
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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414 #set $labels += ["\"%s\"" % ($i.label.value)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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415 #else
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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417 #end if
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418 #end for
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419 </token>
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420
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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421 <xml name="reference_genome_source">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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422 <conditional name="source">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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423 <param name="ref_source" type="select" label="Reference genome">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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424 <option value="cached">locally cached</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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425 <option value="history">in your history</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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426 </param>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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427 <when value="cached">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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428 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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429 <options from_data_table="deepTools_seqs">
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430 <filter type="sort_by" column="1" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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431 <validator type="no_options" message="No indexes are available." />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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432 </options>
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433 </param>
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434 </when>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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435 <when value="history">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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437 </when>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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438 </conditional>
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439 </xml>
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440
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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441 <token name="@reference_genome_source@">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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442 #if $source.ref_source=="history":
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443 --genome $source.input1
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444 #else:
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445 --genome "${source.input1_2bit.fields.path}"
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446 #end if
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447 </token>
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448
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449 <xml name="effectiveGenomeSize">
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450 <conditional name="effectiveGenomeSize">
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451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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452 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.
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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453 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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454 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.">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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455 <option value="93260000">ce10 (93260000)</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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456 <option value="121400000">dm3 (121400000)</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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457 <option value="2451960000" selected="true">hg19 (2451960000)</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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458 <option value="2150570000">mm9 (2150570000)</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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459 <option value="specific">user specified</option>
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460 </param>
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461 <when value="specific">
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462 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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463 </when>
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464 <when value="2150570000" />
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465 <when value="2451960000" />
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466 <when value="121400000" />
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467 <when value="93260000" />
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468 </conditional>
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469 </xml>
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470
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471 <xml name="image_file_format">
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472 <param name="outFileFormat" type="select" label="Image file format">
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473 <option value="png" selected="true">png</option>
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474 <option value="pdf">pdf</option>
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475 <option value="svg">svg</option>
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476 <option value="eps">eps</option>
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477 <option value="emf">emf</option>
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478 </param>
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479 </xml>
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480
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481 <xml name="missingDataAsZero">
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482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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483 label ="Treat missing data as zero"
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484 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." />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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485 </xml>
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486
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487 <xml name="input_save_matrix_values">
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488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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489 </xml>
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490
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491 <xml name="input_graphic_output_settings">
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492 <conditional name="output" >
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493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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494 <option value="no" selected="true">no</option>
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495 <option value="yes">yes</option>
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496 </param>
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497 <when value="no" />
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498 <when value="yes">
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499 <yield />
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500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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501 <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."/>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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502 </when>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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503 </conditional>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
504 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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505
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
506 <xml name="input_image_file_format">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
507 <param name="outFileFormat" type="select" label="Image file format">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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508 <option value="png" selected="true">png</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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509 <option value="pdf">pdf</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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510 <option value="svg">svg</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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511 <option value="eps">eps</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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512 <option value="emf">emf</option>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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513 </param>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
514 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
515
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
516 <xml name="output_image_file_format">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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517 <data format="png" name="outFileName" label="${tool.name} image">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
518 <change_format>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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519 <when input="output.outFileFormat" value="pdf" format="pdf" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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520 <when input="output.outFileFormat" value="svg" format="svg" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
521 <when input="output.outFileFormat" value="eps" format="eps" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
522 <when input="output.outFileFormat" value="emf" format="emf" />
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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523 </change_format>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
524 </data>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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525 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
526
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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527 <xml name="output_save_matrix_values">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
528 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
529 <filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
530 ((
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
531 output['showOutputSettings'] == 'yes' and
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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532 output['saveMatrix'] is True
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
533 ))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
534 </filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
535 </data>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
536 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
537
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
538 <xml name="output_graphic_outputs">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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539 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
540 <filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
541 ((
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
542 output['showOutputSettings'] == 'yes' and
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
543 output['saveData'] is True
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
544 ))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
545 </filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
546 </data>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
547 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
548 <filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
549 ((
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
550 output['showOutputSettings'] == 'yes' and
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
551 output['saveSortedRegions'] is True
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
552 ))
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
553 </filter>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
554 </data>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
555 </xml>
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
556
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
557 <xml name="track_input_h5_macro">
5
b9f41afc3312 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents: 4
diff changeset
558 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
559 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
560 <xml name="track_input_bed_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
561 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
562 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
563 <xml name="track_input_bedgraph_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
564 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
565 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
566 <xml name="track_input_bigwig_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
567 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
568 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
569 <xml name="track_input_bedgraph_matrix_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
570 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
571 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
572 <xml name="track_input_tabular_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
573 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
574 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
575 <xml name="plot_title">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
576 <param name="title" type="text" optional="true" label="Plot title"/>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
577 </xml>
0
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
578
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
579 <xml name="spacer_macro">
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
580 <param name="spacer_width" type="float" value="" optional="True"
8
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 6
diff changeset
581 label="Include spacer at the end of the track." help="Width of the spacer." />
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
582 </xml>
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
583 <xml name="fontsize_macro">
8
c109622e0cf5 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
iuc
parents: 6
diff changeset
584 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
2
2bbe234ca6ce planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
585 </xml>
0
c4ee66c35eb6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
586 </macros>