Mercurial > repos > bgruening > hicexplorer_hictransform

annotate macros.xml @ 7:83fa6254bde1 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:03:27 -0400
parents 74f4f6cbe6ef
children 7c5ad262eaa3
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5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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83fa6254bde1 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
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3 <token name="@WRAPPER_VERSION@">2.1.4</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 <xml name="citations">
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19 <citations>
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20 <citation type="doi">10.5281/zenodo.1133705</citation>
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21 <yield />
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22 </citations>
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23 </xml>
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25 <xml name="zMax">
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26 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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27 </xml>
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28 <xml name="use_range">
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29 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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30 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered.">
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31 <option value="no_use_range">No restriction</option>
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32 <option value="yes_use_range">Only consider counts within a range</option>
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33 </param>
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34 <when value="no_use_range"/>
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35 <when value="yes_use_range">
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36 <expand macro='range' />
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37 </when>
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38 </conditional>
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39 </xml>
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41 <xml name="range">
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42 <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/>
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43 <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/>
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44 </xml>
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45
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46 <xml name="colormap">
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47 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
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48 <option value="RdYlBu">RdYlBu</option>
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49 <option value="Accent">Accent</option>
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50 <option value="Spectral">Spectral</option>
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51 <option value="Set1">Set1</option>
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52 <option value="Set2">Set2</option>
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53 <option value="Set3">Set3</option>
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54 <option value="Dark2">Dark2</option>
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55 <option value="Reds">Reds</option>
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56 <option value="Oranges">Oranges</option>
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57 <option value="Greens">Greens</option>
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58 <option value="Blues">Blues</option>
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59 <option value="Greys">Greys</option>
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60 <option value="Purples">Purples</option>
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61 <option value="Paired">Paired</option>
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62 <option value="Pastel1">Pastel1</option>
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63 <option value="Pastel2">Pastel2</option>
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64 <option value="spring">spring</option>
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65 <option value="summer">summer</option>
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66 <option value="autumn">autumn</option>
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67 <option value="winter">winter</option>
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68 <option value="hot">hot</option>
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69 <option value="coolwarm">coolwarm</option>
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70 <option value="cool">cool</option>
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71 <option value="seismic">seismic</option>
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72 <option value="terrain">terrain</option>
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73 <option value="ocean">ocean</option>
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74 <option value="rainbow">rainbow</option>
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75 <option value="bone">bone</option>
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76 <option value="flag">flag</option>
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77 <option value="prism">prism</option>
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78 <option value="cubehelix">cubehelix</option>
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79 <option value="binary">binary</option>
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80 <option value="pink">pink</option>
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81 <option value="gray">gray</option>
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82 <option value="copper">copper</option>
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83 <option value="BrBG">BrBG</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
84 <option value="BuGn">BuGn</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
85 <option value="BuPu">BuPu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
86 <option value="GnBu">GnBu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
87 <option value="OrRd">OrRd</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
88 <option value="PiYG">PiYG</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
89 <option value="PRGn">PRGn</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
90 <option value="PuOr">PuOr</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
91 <option value="PuRd">PuRd</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
92 <option value="PuBu">PuBu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
93 <option value="RdBu">RdBu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
94 <option value="RdGy">RdGy</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
95 <option value="RdPu">RdPu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
96 <option value="YlGn">YlGn</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
97 <option value="PuBuGn">PuBuGn</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
98 <option value="RdYlGn">RdYlGn</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
99 <option value="YlGnBu">YlGnBu</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
100 <option value="YlOrBr">YlOrBr</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
101 <option value="YlOrRd">YlOrRd</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
102 <option value="gist_gray">gist_gray</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
103 <option value="gist_stern">gist_stern</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
104 <option value="gist_earth">gist_earth</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
105 <option value="gist_yarg">gist_yarg</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
106 <option value="gist_ncar">gist_ncar</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
107 <option value="gist_rainbow">gist_rainbow</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
108 <option value="gist_heat">gist_heat</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
109 <option value="gnuplot">gnuplot</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
110 <option value="gnuplot2">gnuplot2</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
111 <option value="CMRmap">CMRmap</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
112 <option value="bwr">bwr</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
113 <option value="hsv">hsv</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
114 <option value="brg">brg</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
115 <option value="jet">jet</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
116 <option value="afmhot">afmhot</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
117 <option value="Accent_r">Accent reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
118 <option value="Spectral_r">Spectral reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
119 <option value="Set1_r">Set1 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
120 <option value="Set2_r">Set2 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
121 <option value="Set3_r">Set3 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
122 <option value="Dark2_r">Dark2 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
123 <option value="Reds_r">Reds reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
124 <option value="Oranges_r">Oranges reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
125 <option value="Greens_r">Greens reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
126 <option value="Blues_r">Blues reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
127 <option value="Greys_r">Greys reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
128 <option value="Purples_r">Purples reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
129 <option value="Paired_r">Paired reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
130 <option value="Pastel1_r">Pastel1 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
131 <option value="Pastel2_r">Pastel2 reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
132 <option value="spring_r">spring reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
133 <option value="summer_r">summer reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
134 <option value="autumn_r">autumn reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
135 <option value="winter_r">winter reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
136 <option value="hot_r">hot reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
137 <option value="coolwarm_r">coolwarm reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
138 <option value="cool_r">cool reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
139 <option value="seismic_r">seismic reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
140 <option value="terrain_r">terrain reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
141 <option value="ocean_r">ocean reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
142 <option value="rainbow_r">rainbow reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
143 <option value="bone_r">bone reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
144 <option value="flag_r">flag reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
145 <option value="prism_r">prism reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
146 <option value="cubehelix_r">cubehelix reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
147 <option value="binary_r">binary reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
148 <option value="pink_r">pink reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
149 <option value="gray_r">gray reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
150 <option value="copper_r">copper reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
151 <option value="BrBG_r">BrBG reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
152 <option value="BuGn_r">BuGn reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
153 <option value="BuPu_r">BuPu reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
154 <option value="GnBu_r">GnBu reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
155 <option value="OrRd_r">OrRd reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
156 <option value="PiYG_r">PiYG reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
157 <option value="PRGn_r">PRGn reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
158 <option value="PuOr_r">PuOr reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
159 <option value="PuRd_r">PuRd reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
160 <option value="PuBu_r">PuBu reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
161 <option value="RdBu_r">RdBu reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
162 <option value="RdGy_r">RdGy reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
163 <option value="RdPu_r">RdPu reversed</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
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164 <option value="YlGn_r">YlGn reversed</option>
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165 <option value="PuBuGn_r">PuBuGn reversed</option>
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166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
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167 <option value="RdYlGn_r">RdYlGn reversed</option>
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168 <option value="YlGnBu_r">YlGnBu reversed</option>
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169 <option value="YlOrBr_r">YlOrBr reversed</option>
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170 <option value="YlOrRd_r">YlOrRd reversed</option>
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171 <option value="gist_gray_r">gist_gray reversed</option>
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172 <option value="gist_stern_r">gist_stern reversed</option>
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173 <option value="gist_earth_r">gist_earth reversed</option>
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174 <option value="gist_yarg_r">gist_yarg reversed</option>
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175 <option value="gist_ncar_r">gist_ncar reversed</option>
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176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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177 <option value="gist_heat_r">gist_heat reversed</option>
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178 <option value="gnuplot_r">gnuplot reversed</option>
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179 <option value="gnuplot2_r">gnuplot2 reversed</option>
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180 <option value="CMRmap_r">CMRmap reversed</option>
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181 <option value="bwr_r">bwr reversed</option>
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182 <option value="hsv_r">hsv reversed</option>
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183 <option value="brg_r">brg reversed</option>
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184 <option value="jet_r">jet reversed</option>
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185 <option value="afmhot_r">afmhot reversed</option>
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186 </param>
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187 </xml>
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188
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189
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190 <xml name="multiple_input_matrices">
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191 <repeat name="input_files" title="Hi-C Matrix files" min="2">
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192 <param name="matrix" type="data" format="h5,cool"
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193 label="Hi-C Matrix file"
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194 help=""/>
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195 <param name="mlabel" type="text" size="30" optional="true" value=""
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196 label="Label"
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197 help="Label to use in the output. If not given the dataset name will be used instead."/>
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198 </repeat>
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199 </xml>
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200
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201 <token name="@multiple_input_matrices@">
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202 #set $matrices = []
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203 #set $mlabels = []
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204 #for $counter, $i in enumerate($input_files):
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205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
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206 #silent $matrices.append( '%s_matrix' % $counter )
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207
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208 #if str($i.mlabel.value) != "":
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209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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210 #else
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211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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212 #end if
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213 #end for
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214 #set $mlabels = ' '.join($mlabels)
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215 #set $matrices = ' '.join($matrices)
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216 </token>
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217
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218
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219 <xml name="region">
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220 <param name="region" type="text" label="Region of the genome to limit the operation"
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221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
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222 </xml>
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223
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224
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225
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226 <xml name="kmeans_clustering">
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227 <conditional name="used_multiple_regions">
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228 <param name="used_multiple_regions_options" type="select"
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229 label="Did you compute the matrix with more than one groups of regions?"
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230 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
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231 <option value="yes">Yes, I used multiple groups of regions</option>
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232 <option value="no">No, I used only one group</option>
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233 </param>
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234 <when value="no">
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235 <conditional name="clustering">
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236 <param name="clustering_options" type="select" label="Clustering algorithm">
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237 <option value="none">No clustering</option>
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238 <option value="kmeans">Kmeans clustering</option>
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239 </param>
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240 <when value="kmeans">
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241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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242 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
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243 </when>
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244 <when value="none" />
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245 </conditional>
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246 </when>
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247 <when value="yes" />
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248 </conditional>
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249 </xml>
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250
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251 <token name="@KMEANS_CLUSTERING@">
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252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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256 #end if
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257 #end if
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258 #end if
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259 </token>
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260
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261 <xml name="samFlag">
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262 <param name="samFlag" type="integer" optional="true" value=""
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263 label="Filter reads based on the SAM flag"
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264 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
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265 </xml>
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266 <xml name="plotNumbers">
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267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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268 label="Plot the correlation value"
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269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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270 </xml>
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271 <xml name="doNotExtendPairedEnds">
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272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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273 label="Do not extend paired ends"
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274 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
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275 </xml>
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276
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277 <xml name="ignoreDuplicates">
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278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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279 label="Ignore duplicates"
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280 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
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281 </xml>
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282
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283 <xml name="minMappingQuality">
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284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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285 label="Minimum mapping quality"
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286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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288 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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289 </xml>
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290
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291 <xml name="skipZeros">
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292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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293 label ="Skip zeros"
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294 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
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295 </xml>
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296
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297 <xml name="fragmentLength">
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298 <param name="fragmentLength" type="integer" value="300" min="1"
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299 label="Fragment length used for the sequencing"
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300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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301 </xml>
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302
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303 <xml name="scaleFactor">
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304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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306 </xml>
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307
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308 <xml name="xMax">
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309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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310 label="Max value for the x-axis in counts per bin" />
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311 </xml>
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312
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313 <xml name="filterThreshold">
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314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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316
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317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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319 </xml>
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320
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321
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322 <xml name="pseudocount">
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323 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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324 </xml>
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325 <xml name='matrix_h5_cooler_macro'>
3
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326 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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327 label="Matrix to compute on"/>
0
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328 </xml>
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329 <xml name='matrix_h5_cooler_multiple_macro'>
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330 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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331 label="Matricies to compute on" multiple="true"/>
0
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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332 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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333 <token name="@REFERENCES@">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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334
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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335 .. class:: infomark
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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336
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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337 For more information on the tools, please visit our `help site`_.
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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338
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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339 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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340
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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341 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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342
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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343 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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344 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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345 .. _help site: https://hicexplorer.readthedocs.org
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346
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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347 </token>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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348
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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349
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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350 <xml name="multiple_input_bams">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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351 <repeat name="input_files" title="BAM files" min="2">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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352 <param name="bamfile" type="data" format="bam"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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353 label="Bam file"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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354 help="The BAM file must be sorted."/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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355 <param name="label" type="text" size="30" optional="true" value=""
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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356 label="Label"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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357 help="Label to use in the output. If not given the dataset name will be used instead."/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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358 </repeat>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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359 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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360
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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361 <xml name="multiple_input_bigwigs">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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362 <repeat name="input_files" title="BigWig files" min="2">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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363 <param name="bigwigfile" type="data" format="bigwig"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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364 label="Bigwig file"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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365 help="The Bigwig file must be sorted."/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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366 <param name="label" type="text" size="30" optional="true" value=""
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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367 label="Label"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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368 help="Label to use in the output. If not given the dataset name will be used instead."/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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369 </repeat>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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370 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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371
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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372 <xml name="plotTitle">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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373 <param name="plotTitle" type="text" value="" size="30" optional="True"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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374 label="Title of the plot"
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375 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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376 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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377
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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378 <token name="@multiple_input_bams@">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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379 #import tempfile
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380 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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381 #set files=[]
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382 #set labels=[]
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383 #for $i in $input_files:
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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384 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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385 #set $temp_input_path = $temp_input_handle.name
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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386 #silent $temp_input_handle.close()
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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387 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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388 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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389 #silent $files.append('%s.bam' % $temp_input_path)
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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390
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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391 ##set $files += [str($i.bamfile)]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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392 #if str($i.label.value) != "":
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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393 #set $labels += ["\"%s\"" % ($i.label.value)]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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394 #else
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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395 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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396 #end if
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397 #end for
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398 </token>
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399
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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400 <token name="@multiple_input_bigwigs@">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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401 #import tempfile
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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402 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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403 #set files=[]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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404 #set labels=[]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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405 #for $i in $input_files:
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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406 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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407 #set $temp_input_path = $temp_input_handle.name
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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408 #silent $temp_input_handle.close()
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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409 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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410 #silent $files.append('%s.bw' % $temp_input_path)
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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411
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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412 ##set $files += [str($i.bigwigfile)]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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413 #if str($i.label.value) != "":
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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414 #set $labels += ["\"%s\"" % ($i.label.value)]
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415 #else
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416 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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417 #end if
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418 #end for
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419 </token>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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420
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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421 <xml name="reference_genome_source">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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422 <conditional name="source">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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423 <param name="ref_source" type="select" label="Reference genome">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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424 <option value="cached">locally cached</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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425 <option value="history">in your history</option>
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426 </param>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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427 <when value="cached">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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428 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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429 <options from_data_table="deepTools_seqs">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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430 <filter type="sort_by" column="1" />
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431 <validator type="no_options" message="No indexes are available." />
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432 </options>
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433 </param>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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434 </when>
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435 <when value="history">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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436 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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437 </when>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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438 </conditional>
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439 </xml>
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440
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441 <token name="@reference_genome_source@">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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442 #if $source.ref_source=="history":
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443 --genome $source.input1
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444 #else:
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445 --genome "${source.input1_2bit.fields.path}"
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446 #end if
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447 </token>
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448
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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449 <xml name="effectiveGenomeSize">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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450 <conditional name="effectiveGenomeSize">
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451 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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452 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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453 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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454 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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455 <option value="93260000">ce10 (93260000)</option>
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456 <option value="121400000">dm3 (121400000)</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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457 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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458 <option value="2150570000">mm9 (2150570000)</option>
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459 <option value="specific">user specified</option>
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460 </param>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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461 <when value="specific">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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462 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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463 </when>
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464 <when value="2150570000" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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465 <when value="2451960000" />
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466 <when value="121400000" />
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467 <when value="93260000" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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468 </conditional>
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469 </xml>
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470
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471 <xml name="image_file_format">
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472 <param name="outFileFormat" type="select" label="Image file format">
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473 <option value="png" selected="true">png</option>
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474 <option value="pdf">pdf</option>
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475 <option value="svg">svg</option>
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476 <option value="eps">eps</option>
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477 <option value="emf">emf</option>
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478 </param>
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479 </xml>
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480
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481 <xml name="missingDataAsZero">
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482 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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483 label ="Treat missing data as zero"
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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484 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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485 </xml>
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486
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487 <xml name="input_save_matrix_values">
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488 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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489 </xml>
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490
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491 <xml name="input_graphic_output_settings">
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492 <conditional name="output" >
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493 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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494 <option value="no" selected="true">no</option>
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495 <option value="yes">yes</option>
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496 </param>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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497 <when value="no" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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498 <when value="yes">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
499 <yield />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
500 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
501 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
502 </when>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
503 </conditional>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
504 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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diff changeset
505
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
506 <xml name="input_image_file_format">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
507 <param name="outFileFormat" type="select" label="Image file format">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
508 <option value="png" selected="true">png</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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509 <option value="pdf">pdf</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
510 <option value="svg">svg</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
511 <option value="eps">eps</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
512 <option value="emf">emf</option>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
513 </param>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
514 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
515
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
516 <xml name="output_image_file_format">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
517 <data format="png" name="outFileName" label="${tool.name} image">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
518 <change_format>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
519 <when input="output.outFileFormat" value="pdf" format="pdf" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
520 <when input="output.outFileFormat" value="svg" format="svg" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
521 <when input="output.outFileFormat" value="eps" format="eps" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
522 <when input="output.outFileFormat" value="emf" format="emf" />
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
523 </change_format>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
524 </data>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
525 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
526
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
527 <xml name="output_save_matrix_values">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
528 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
529 <filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
530 ((
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
531 output['showOutputSettings'] == 'yes' and
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
532 output['saveMatrix'] is True
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
533 ))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
534 </filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
535 </data>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
536 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
537
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
538 <xml name="output_graphic_outputs">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
539 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
540 <filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
541 ((
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
542 output['showOutputSettings'] == 'yes' and
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
543 output['saveData'] is True
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
544 ))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
545 </filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
546 </data>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
547 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
548 <filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
parents:
diff changeset
549 ((
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
550 output['showOutputSettings'] == 'yes' and
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
551 output['saveSortedRegions'] is True
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
552 ))
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
553 </filter>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
554 </data>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
555 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
556
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
557 <xml name="track_input_h5_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
558 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
559 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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parents:
diff changeset
560 <xml name="track_input_bed_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
561 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
562 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
563 <xml name="track_input_bedgraph_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
564 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
565 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
566 <xml name="track_input_bigwig_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
567 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
568 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
569 <xml name="track_input_bedgraph_matrix_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
570 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
571 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
572 <xml name="track_input_tabular_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
573 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
bgruening
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diff changeset
574 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
575 <xml name="plot_title">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
576 <param name="title" type="text" optional="true" label="Plot title"/>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
577 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
578
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
579 <xml name="spacer_macro">
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
580 <param name="spacer_width" type="float" value="" optional="True"
3
778158ebfddd planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
581 label="Include spacer at the end of the track." help="Width of the spacer." />
0
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
582 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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diff changeset
583 <xml name="fontsize_macro">
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584 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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585 </xml>
5c869935cf2b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
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586 </macros>