annotate macros.xml @ 7:5e9c304c424c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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date Mon, 16 Dec 2019 15:42:31 -0500
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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3 <token name="@WRAPPER_VERSION@">3.3.1</token>
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4 <token name="@USE_RANGE@">
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5 #if $use_range.select_use_range == "yes_use_range":
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6 --range $range_min:$range_max
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7 #end if
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8 </token>
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9
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10 <xml name="requirements">
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11 <requirements>
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12 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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13 <yield />
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14 </requirements>
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15 <version_command>@BINARY@ --version</version_command>
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16 </xml>
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18 <token name="@CHROMOSOME_LIST@">
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19 #if $chromosome_list:
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20 #set $chromosomes = []
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21 #for $chrom in $chromosome_list:
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22 #silent $chromosomes.append("'%s'" % $chrom.chromosomes)
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23 #end for
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24 #set $chromosome_string = ' '.join($chromosomes)
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25 --chromosomes $chromosome_string
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26 #end if
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27 </token>
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29 <xml name="chromosome_list">
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30 <repeat name="chromosome_list" min="0" title="Chromosomes to include" help="Chromosomes to include in the analysis. If not set, all chromosomes are included.">
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31 <param argument="--chromosomes" type="text" value="" >
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32 <validator type="empty_field" />
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33 </param>
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34 </repeat>
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35 </xml>
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36
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37 <xml name="citations">
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38 <citations>
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39 <citation type="doi">10.5281/zenodo.1133705</citation>
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40 <yield />
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41 </citations>
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42 </xml>
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44 <xml name="zMax">
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45 <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 -->
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46 </xml>
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47 <xml name="use_range">
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48 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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49 <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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50 <option value="no_use_range">No restriction</option>
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51 <option value="yes_use_range">Only consider counts within a range</option>
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52 </param>
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53 <when value="no_use_range"/>
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54 <when value="yes_use_range">
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55 <expand macro='range' />
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="range">
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61 <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."/>
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62 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
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63 </xml>
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64
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65 <xml name="colormap">
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66 <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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67 <option value="RdYlBu">RdYlBu</option>
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68 <option value="Accent">Accent</option>
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69 <option value="Spectral">Spectral</option>
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70 <option value="Set1">Set1</option>
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71 <option value="Set2">Set2</option>
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72 <option value="Set3">Set3</option>
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73 <option value="Dark2">Dark2</option>
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74 <option value="Reds">Reds</option>
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75 <option value="Oranges">Oranges</option>
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76 <option value="Greens">Greens</option>
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77 <option value="Blues">Blues</option>
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78 <option value="Greys">Greys</option>
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79 <option value="Purples">Purples</option>
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80 <option value="Paired">Paired</option>
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81 <option value="Pastel1">Pastel1</option>
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82 <option value="Pastel2">Pastel2</option>
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83 <option value="spring">spring</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
84 <option value="summer">summer</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
85 <option value="autumn">autumn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
86 <option value="winter">winter</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
87 <option value="hot">hot</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
88 <option value="coolwarm">coolwarm</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
89 <option value="cool">cool</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
90 <option value="seismic">seismic</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
91 <option value="terrain">terrain</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
92 <option value="ocean">ocean</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
93 <option value="rainbow">rainbow</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
94 <option value="bone">bone</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
95 <option value="flag">flag</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
96 <option value="prism">prism</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
97 <option value="cubehelix">cubehelix</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
98 <option value="binary">binary</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
99 <option value="pink">pink</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
100 <option value="gray">gray</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
101 <option value="copper">copper</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
102 <option value="BrBG">BrBG</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
103 <option value="BuGn">BuGn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
104 <option value="BuPu">BuPu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
105 <option value="GnBu">GnBu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
106 <option value="OrRd">OrRd</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
107 <option value="PiYG">PiYG</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
108 <option value="PRGn">PRGn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
109 <option value="PuOr">PuOr</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
110 <option value="PuRd">PuRd</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
111 <option value="PuBu">PuBu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
112 <option value="RdBu">RdBu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
113 <option value="RdGy">RdGy</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
114 <option value="RdPu">RdPu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
115 <option value="YlGn">YlGn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
116 <option value="PuBuGn">PuBuGn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
117 <option value="RdYlGn">RdYlGn</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
118 <option value="YlGnBu">YlGnBu</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
119 <option value="YlOrBr">YlOrBr</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
120 <option value="YlOrRd">YlOrRd</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
121 <option value="gist_gray">gist_gray</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
122 <option value="gist_stern">gist_stern</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
123 <option value="gist_earth">gist_earth</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
124 <option value="gist_yarg">gist_yarg</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
125 <option value="gist_ncar">gist_ncar</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
126 <option value="gist_rainbow">gist_rainbow</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
127 <option value="gist_heat">gist_heat</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
128 <option value="gnuplot">gnuplot</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
129 <option value="gnuplot2">gnuplot2</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
130 <option value="CMRmap">CMRmap</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
131 <option value="bwr">bwr</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
132 <option value="hsv">hsv</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
133 <option value="brg">brg</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
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134 <option value="jet">jet</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
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135 <option value="afmhot">afmhot</option>
7
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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parents: 5
diff changeset
136 <option value="plasma">plasma</option>
0
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
137 <option value="Accent_r">Accent reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
138 <option value="Spectral_r">Spectral reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
139 <option value="Set1_r">Set1 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
140 <option value="Set2_r">Set2 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
141 <option value="Set3_r">Set3 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
142 <option value="Dark2_r">Dark2 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
143 <option value="Reds_r">Reds reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
144 <option value="Oranges_r">Oranges reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
145 <option value="Greens_r">Greens reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
146 <option value="Blues_r">Blues reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
147 <option value="Greys_r">Greys reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
148 <option value="Purples_r">Purples reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
149 <option value="Paired_r">Paired reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
150 <option value="Pastel1_r">Pastel1 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
151 <option value="Pastel2_r">Pastel2 reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
152 <option value="spring_r">spring reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
153 <option value="summer_r">summer reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
154 <option value="autumn_r">autumn reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
155 <option value="winter_r">winter reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
156 <option value="hot_r">hot reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
157 <option value="coolwarm_r">coolwarm reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
158 <option value="cool_r">cool reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
159 <option value="seismic_r">seismic reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
160 <option value="terrain_r">terrain reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
161 <option value="ocean_r">ocean reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
162 <option value="rainbow_r">rainbow reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
163 <option value="bone_r">bone reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
164 <option value="flag_r">flag reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
165 <option value="prism_r">prism reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
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166 <option value="cubehelix_r">cubehelix reversed</option>
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167 <option value="binary_r">binary reversed</option>
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168 <option value="pink_r">pink reversed</option>
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169 <option value="gray_r">gray reversed</option>
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170 <option value="copper_r">copper reversed</option>
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171 <option value="BrBG_r">BrBG reversed</option>
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172 <option value="BuGn_r">BuGn reversed</option>
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173 <option value="BuPu_r">BuPu reversed</option>
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174 <option value="GnBu_r">GnBu reversed</option>
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175 <option value="OrRd_r">OrRd reversed</option>
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176 <option value="PiYG_r">PiYG reversed</option>
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177 <option value="PRGn_r">PRGn reversed</option>
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178 <option value="PuOr_r">PuOr reversed</option>
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179 <option value="PuRd_r">PuRd reversed</option>
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180 <option value="PuBu_r">PuBu reversed</option>
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181 <option value="RdBu_r">RdBu reversed</option>
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182 <option value="RdGy_r">RdGy reversed</option>
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183 <option value="RdPu_r">RdPu reversed</option>
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184 <option value="YlGn_r">YlGn reversed</option>
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185 <option value="PuBuGn_r">PuBuGn reversed</option>
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186 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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187 <option value="RdYlGn_r">RdYlGn reversed</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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188 <option value="YlGnBu_r">YlGnBu reversed</option>
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189 <option value="YlOrBr_r">YlOrBr reversed</option>
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190 <option value="YlOrRd_r">YlOrRd reversed</option>
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191 <option value="gist_gray_r">gist_gray reversed</option>
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192 <option value="gist_stern_r">gist_stern reversed</option>
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193 <option value="gist_earth_r">gist_earth reversed</option>
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194 <option value="gist_yarg_r">gist_yarg reversed</option>
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195 <option value="gist_ncar_r">gist_ncar reversed</option>
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196 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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197 <option value="gist_heat_r">gist_heat reversed</option>
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198 <option value="gnuplot_r">gnuplot reversed</option>
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199 <option value="gnuplot2_r">gnuplot2 reversed</option>
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200 <option value="CMRmap_r">CMRmap reversed</option>
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201 <option value="bwr_r">bwr reversed</option>
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202 <option value="hsv_r">hsv reversed</option>
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203 <option value="brg_r">brg reversed</option>
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204 <option value="jet_r">jet reversed</option>
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205 <option value="afmhot_r">afmhot reversed</option>
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206 <option value="plasma_r">plasma reversed</option>
0
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207 </param>
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208 </xml>
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209
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210 <xml name="multiple_input_matrices">
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211 <repeat name="input_files" title="Hi-C Matrix files" min="2">
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212 <param name="matrix" type="data" format="h5,cool"
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213 label="Hi-C Matrix file"
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214 help=""/>
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215 <param name="mlabel" type="text" size="30" optional="true" value=""
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216 label="Label"
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217 help="Label to use in the output. If not given the dataset name will be used instead."/>
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218 </repeat>
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219 </xml>
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220
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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221 <token name="@multiple_input_matrices@">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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222 #set $matrices = []
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223 #set $mlabels = []
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224 #for $counter, $i in enumerate($input_files):
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225 ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
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226 #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
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227
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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228 #if str($i.mlabel.value) != "":
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229 #set $mlabels += ['\'%s\'' % ($i.mlabel.value)]
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230 #else
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231 #set $mlabels += ['\'%s\'' % ($i.matrix.name)]
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232 #end if
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233 #end for
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234 #set $mlabels = ' '.join($mlabels)
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235 #set $matrices = ' '.join($matrices)
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236 </token>
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237
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238 <token name="@ESCAPE_IDENTIFIER_FILE@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($file.element_identifier))]]></token>
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239 <token name="@ESCAPE_IDENTIFIER_MATRIX@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($matrix.element_identifier))]]></token>
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240 <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token>
0
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241
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242 <xml name="region">
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243 <param name="region" type="text" label="Region of the genome to limit the operation"
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244 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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245 </xml>
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246
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247
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248
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249 <xml name="kmeans_clustering">
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250 <conditional name="used_multiple_regions">
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251 <param name="used_multiple_regions_options" type="select"
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252 label="Did you compute the matrix with more than one groups of regions?"
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253 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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254 <option value="yes">Yes, I used multiple groups of regions</option>
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255 <option value="no">No, I used only one group</option>
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256 </param>
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257 <when value="no">
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258 <conditional name="clustering">
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259 <param name="clustering_options" type="select" label="Clustering algorithm">
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260 <option value="none">No clustering</option>
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261 <option value="kmeans">Kmeans clustering</option>
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262 </param>
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263 <when value="kmeans">
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264 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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265 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
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266 </when>
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267 <when value="none" />
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268 </conditional>
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269 </when>
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270 <when value="yes" />
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271 </conditional>
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272 </xml>
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273
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274 <token name="@KMEANS_CLUSTERING@">
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275 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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276 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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277 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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278 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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279 #end if
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280 #end if
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281 #end if
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282 </token>
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283
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284 <xml name="samFlag">
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285 <param name="samFlag" type="integer" optional="true" value=""
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286 label="Filter reads based on the SAM flag"
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287 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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288 </xml>
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289 <xml name="plotNumbers">
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290 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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291 label="Plot the correlation value"
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292 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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293 </xml>
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294 <xml name="doNotExtendPairedEnds">
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295 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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296 label="Do not extend paired ends"
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297 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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298 </xml>
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299
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300 <xml name="ignoreDuplicates">
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301 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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302 label="Ignore duplicates"
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303 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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304 </xml>
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305
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306 <xml name="minMappingQuality">
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307 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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308 label="Minimum mapping quality"
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309 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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310 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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311 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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312 </xml>
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313
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314 <xml name="skipZeros">
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315 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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316 label ="Skip zeros"
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317 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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318 </xml>
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319
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320 <xml name="fragmentLength">
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321 <param name="fragmentLength" type="integer" value="300" min="1"
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322 label="Fragment length used for the sequencing"
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323 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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324 </xml>
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325
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326 <xml name="scaleFactor">
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327 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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328 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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329 </xml>
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330
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331 <xml name="xMax">
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332 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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333 label="Max value for the x-axis in counts per bin" />
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334 </xml>
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335
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336 <xml name="filterThreshold">
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337 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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338 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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339
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340 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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341 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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342 </xml>
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343
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344
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345 <xml name="pseudocount">
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346 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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347 </xml>
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348 <xml name='matrix_h5_cooler_macro'>
2
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349 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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350 label="Matrix to compute on"/>
0
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351 </xml>
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352 <xml name='matrix_h5_cooler_multiple_macro'>
2
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353 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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354 label="Matricies to compute on" multiple="true"/>
0
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355 </xml>
7
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356
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357
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358
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359 <xml name='convertFormat_single_macro'>
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360 <conditional name="inputFormat_conditional">
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361 <param name="inputFormat_selector" type="select" label="Choose input file type">
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362 <option value="optionCool" selected="True">cool</option>
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363 <option value="optionH5">h5</option>
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364 <!-- <option value="optionHic">hic</option> -->
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365 <option value="optionHomer">Homer</option>
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366 <option value="optionHicpro">HiCPro</option>
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367 </param>
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368 <when value="optionCool">
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369 <expand macro='matrix_h5_cooler_macro' />
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370 <param name='correctionName' type='text' label='Correction factors column name'/>
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371 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
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372 <param name='chromosome' type='text' label='Load only one chromosome'/>
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373 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
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374
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375 </when>
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376 <when value="optionH5">
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377 <expand macro='matrix_h5_cooler_macro' />
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378 </when>
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379 <!-- <when value="optionHic">
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380 <param name='matrixHic' type='data' format='binary' label='.hic matrix'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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381 <param name='resolutions' type='text' label='List of resolutions'/>
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382 </when> -->
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383
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384 <when value="optionHomer">
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385 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix'/>
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386 </when>
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387
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388 <when value="optionHicpro">
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389 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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390 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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391 </when>
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392 </conditional>
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393 </xml>
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394
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395 <xml name='convertFormat_multiple_macro'>
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396 <conditional name="inputFormat_conditional">
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397 <param name="inputFormat_selector" type="select" label="Choose input file type">
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398 <option value="optionCool" selected="True">cool</option>
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399 <option value="optionH5">h5</option>
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400 <option value="optionHomer">Homer</option>
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401 <option value="optionHicpro">HiCPro</option>
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402 </param>
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403 <when value="optionCool">
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404 <expand macro='matrix_h5_cooler_multiple_macro' />
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405 <param name='correctionName' type='text' label='Correction factors column name'/>
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406 <param name='correctionDivision' type="boolean" truevalue="yes" falsevalue="" label='Apply correction factors with a division instead multiplication'/>
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407 <param name='chromosome' type='text' label='Load only one chromosome'/>
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408 <param name='loadRawValues' type="boolean" truevalue="yes" falsevalue="" label='Load raw data'/>
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409
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410 </when>
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411 <when value="optionH5">
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412 <expand macro='matrix_h5_cooler_multiple_macro' />
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413 </when>
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414
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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415 <when value="optionHomer">
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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416 <param name='matrixHomer' type='data' format='txt' label='Homer interaction matrix' multiple="true"/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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417 </when>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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418
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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419 <when value="optionHicpro">
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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420 <param name='matrixHicpro' type='data' format='txt' label='.hic matrix' multiple="true"/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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421 <param name='bedHicpro' type='data' format='bed' label='HicPro bed file' multiple="true"/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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422 </when>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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423 </conditional>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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424 </xml>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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425 <xml name='convertFormat_single_output_macro'>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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426 <!-- <filter>outputSingleMultiple_conditional.inputFormat_conditional.inputFormat_selector == 'optionCool'</filter> -->
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
427
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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428 <conditional name="outputFormat_conditional">
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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429 <param name="outputFormat_selector" type="select" label="Choose output file type">
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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430 <option value="cool" selected="True">cool</option>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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431 <option value="h5">h5</option>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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432 <option value="homer">Homer</option>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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433 <option value="ginteractions">ginteractions</option>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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434
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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diff changeset
435 </param>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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436 <when value="cool">
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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437 <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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438 <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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439 </when>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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440 <when value='h5'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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441 <when value='homer'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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442 <when value='ginteractions'/>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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443
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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444 </conditional>
5e9c304c424c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
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445 </xml>
0
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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446 <token name="@REFERENCES@">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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447
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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448 .. class:: infomark
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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449
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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450 For more information on the tools, please visit our `help site`_.
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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451
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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452 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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453
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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454 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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455
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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456 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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457 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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458 .. _help site: https://hicexplorer.readthedocs.org
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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459
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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460 </token>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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461
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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462
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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463 <xml name="multiple_input_bams">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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464 <repeat name="input_files" title="BAM files" min="2">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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465 <param name="bamfile" type="data" format="bam"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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466 label="Bam file"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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467 help="The BAM file must be sorted."/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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468 <param name="label" type="text" size="30" optional="true" value=""
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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469 label="Label"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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470 help="Label to use in the output. If not given the dataset name will be used instead."/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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471 </repeat>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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472 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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473
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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474 <xml name="multiple_input_bigwigs">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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475 <repeat name="input_files" title="BigWig files" min="2">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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476 <param name="bigwigfile" type="data" format="bigwig"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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477 label="Bigwig file"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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478 help="The Bigwig file must be sorted."/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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479 <param name="label" type="text" size="30" optional="true" value=""
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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480 label="Label"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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481 help="Label to use in the output. If not given the dataset name will be used instead."/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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482 </repeat>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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483 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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484
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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485 <xml name="plotTitle">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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486 <param name="plotTitle" type="text" value="" size="30" optional="True"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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487 label="Title of the plot"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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488 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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489 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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490
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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491 <token name="@multiple_input_bams@">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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492 #import tempfile
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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493 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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494 #set files=[]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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495 #set labels=[]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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496 #for $i in $input_files:
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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497 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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498 #set $temp_input_path = $temp_input_handle.name
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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499 #silent $temp_input_handle.close()
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
500 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
501 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
502 #silent $files.append('%s.bam' % $temp_input_path)
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
503
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
504 ##set $files += [str($i.bamfile)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
505 #if str($i.label.value) != "":
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
506 #set $labels += ["\"%s\"" % ($i.label.value)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
507 #else
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
508 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
509 #end if
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
510 #end for
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
511 </token>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
512
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
513 <token name="@multiple_input_bigwigs@">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
514 #import tempfile
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
515 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
516 #set files=[]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
517 #set labels=[]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
518 #for $i in $input_files:
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
519 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
520 #set $temp_input_path = $temp_input_handle.name
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
521 #silent $temp_input_handle.close()
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
522 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
523 #silent $files.append('%s.bw' % $temp_input_path)
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
524
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
525 ##set $files += [str($i.bigwigfile)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
526 #if str($i.label.value) != "":
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
527 #set $labels += ["\"%s\"" % ($i.label.value)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
528 #else
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
529 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
530 #end if
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
531 #end for
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
532 </token>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
533
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
534 <xml name="reference_genome_source">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
535 <conditional name="source">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
536 <param name="ref_source" type="select" label="Reference genome">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
537 <option value="cached">locally cached</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
538 <option value="history">in your history</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
539 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
540 <when value="cached">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
541 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
542 <options from_data_table="deepTools_seqs">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
543 <filter type="sort_by" column="1" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
544 <validator type="no_options" message="No indexes are available." />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
545 </options>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
546 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
547 </when>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
548 <when value="history">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
549 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
550 </when>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
551 </conditional>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
552 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
553
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
554 <token name="@reference_genome_source@">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
555 #if $source.ref_source=="history":
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
556 --genome $source.input1
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
557 #else:
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
558 --genome "${source.input1_2bit.fields.path}"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
559 #end if
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
560 </token>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
561
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
562 <xml name="effectiveGenomeSize">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
563 <conditional name="effectiveGenomeSize">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
564 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
565 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.
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
566 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
567 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.">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
568 <option value="93260000">ce10 (93260000)</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
569 <option value="121400000">dm3 (121400000)</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
570 <option value="2451960000" selected="true">hg19 (2451960000)</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
571 <option value="2150570000">mm9 (2150570000)</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
572 <option value="specific">user specified</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
573 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
574 <when value="specific">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
575 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
576 </when>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
577 <when value="2150570000" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
578 <when value="2451960000" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
579 <when value="121400000" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
580 <when value="93260000" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
581 </conditional>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
582 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
583
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
584 <xml name="image_file_format">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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585 <param name="outFileFormat" type="select" label="Image file format">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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586 <option value="png" selected="true">png</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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587 <option value="pdf">pdf</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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588 <option value="svg">svg</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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589 <option value="eps">eps</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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590 <option value="emf">emf</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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591 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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592 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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593
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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594 <xml name="missingDataAsZero">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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595 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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596 label ="Treat missing data as zero"
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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597 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." />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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598 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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599
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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600 <xml name="input_save_matrix_values">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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601 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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602 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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603
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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604 <xml name="input_graphic_output_settings">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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605 <conditional name="output" >
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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606 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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607 <option value="no" selected="true">no</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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608 <option value="yes">yes</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
609 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
610 <when value="no" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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611 <when value="yes">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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612 <yield />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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613 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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614 <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."/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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615 </when>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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616 </conditional>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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617 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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618
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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619 <xml name="input_image_file_format">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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620 <param name="outFileFormat" type="select" label="Image file format">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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621 <option value="png" selected="true">png</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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622 <option value="pdf">pdf</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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623 <option value="svg">svg</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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624 <option value="eps">eps</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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625 <option value="emf">emf</option>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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626 </param>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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627 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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628
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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629 <xml name="output_image_file_format">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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630 <data format="png" name="outFileName" label="${tool.name} image">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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631 <change_format>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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632 <when input="output.outFileFormat" value="pdf" format="pdf" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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633 <when input="output.outFileFormat" value="svg" format="svg" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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634 <when input="output.outFileFormat" value="eps" format="eps" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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635 <when input="output.outFileFormat" value="emf" format="emf" />
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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636 </change_format>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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637 </data>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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638 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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639
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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640 <xml name="output_save_matrix_values">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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641 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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642 <filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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643 ((
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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644 output['showOutputSettings'] == 'yes' and
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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645 output['saveMatrix'] is True
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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646 ))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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647 </filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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648 </data>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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649 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
650
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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651 <xml name="output_graphic_outputs">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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652 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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653 <filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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654 ((
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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655 output['showOutputSettings'] == 'yes' and
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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656 output['saveData'] is True
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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657 ))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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658 </filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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659 </data>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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660 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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661 <filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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662 ((
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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663 output['showOutputSettings'] == 'yes' and
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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664 output['saveSortedRegions'] is True
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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665 ))
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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666 </filter>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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667 </data>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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668 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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669
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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670 <xml name="track_input_h5_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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671 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
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672 </xml>
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673 <xml name="track_input_bed_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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674 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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675 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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676 <xml name="track_input_bedgraph_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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677 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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678 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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679 <xml name="track_input_bigwig_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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680 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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681 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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682 <xml name="track_input_bedgraph_matrix_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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683 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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684 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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685 <xml name="track_input_tabular_macro">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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686 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
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687 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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688 <xml name="plot_title">
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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689 <param name="title" type="text" optional="true" label="Plot title"/>
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690 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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691
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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692 <xml name="spacer_macro">
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693 <param name="spacer_width" type="float" value="" optional="True"
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694 label="Include spacer at the end of the track." help="Width of the spacer." />
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695 </xml>
58d146c74d72 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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696 <xml name="fontsize_macro">
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697 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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698 </xml>
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699 </macros>