Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate macros.xml @ 4:e8d6e15adc5d draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
author iuc
date Mon, 27 Nov 2017 08:38:43 -0500
parents 7c2c17b2c4a6
children f1482e1a225a
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70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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1 <macros>
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iuc
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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e8d6e15adc5d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 1beb50fdb3f5f8fd60e3b9c3d44964d70075616d
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3 <token name="@WRAPPER_VERSION@">1.8.1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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7 <yield />
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8 </requirements>
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9 <version_command>@BINARY@ --version</version_command>
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10 </xml>
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12 <xml name="citations">
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13 <citations>
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14 <citation type="doi">10.5281/zenodo.159780</citation>
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15 <yield />
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16 </citations>
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17 </xml>
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19 <xml name="zMax">
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20 <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->
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21 </xml>
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22
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23 <xml name="colormap">
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24 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
8116270ba934 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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25 <option value="RdYlBu">RdYlBu</option>
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26 <option value="Accent">Accent</option>
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27 <option value="Spectral">Spectral</option>
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28 <option value="Set1">Set1</option>
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29 <option value="Set2">Set2</option>
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30 <option value="Set3">Set3</option>
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31 <option value="Dark2">Dark2</option>
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32 <option value="Reds">Reds</option>
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33 <option value="Oranges">Oranges</option>
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34 <option value="Greens">Greens</option>
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35 <option value="Blues">Blues</option>
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36 <option value="Greys">Greys</option>
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37 <option value="Purples">Purples</option>
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38 <option value="Paired">Paired</option>
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39 <option value="Pastel1">Pastel1</option>
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40 <option value="Pastel2">Pastel2</option>
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41 <option value="spring">spring</option>
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42 <option value="summer">summer</option>
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43 <option value="autumn">autumn</option>
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44 <option value="winter">winter</option>
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45 <option value="hot">hot</option>
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46 <option value="coolwarm">coolwarm</option>
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47 <option value="cool">cool</option>
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48 <option value="seismic">seismic</option>
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49 <option value="terrain">terrain</option>
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50 <option value="ocean">ocean</option>
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51 <option value="rainbow">rainbow</option>
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52 <option value="bone">bone</option>
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53 <option value="flag">flag</option>
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54 <option value="prism">prism</option>
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55 <option value="cubehelix">cubehelix</option>
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56 <option value="binary">binary</option>
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57 <option value="pink">pink</option>
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58 <option value="gray">gray</option>
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59 <option value="copper">copper</option>
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60 <option value="BrBG">BrBG</option>
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61 <option value="BuGn">BuGn</option>
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62 <option value="BuPu">BuPu</option>
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63 <option value="GnBu">GnBu</option>
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64 <option value="OrRd">OrRd</option>
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65 <option value="PiYG">PiYG</option>
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66 <option value="PRGn">PRGn</option>
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67 <option value="PuOr">PuOr</option>
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68 <option value="PuRd">PuRd</option>
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69 <option value="PuBu">PuBu</option>
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70 <option value="RdBu">RdBu</option>
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71 <option value="RdGy">RdGy</option>
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72 <option value="RdPu">RdPu</option>
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73 <option value="YlGn">YlGn</option>
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74 <option value="PuBuGn">PuBuGn</option>
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75 <option value="RdYlGn">RdYlGn</option>
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76 <option value="YlGnBu">YlGnBu</option>
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77 <option value="YlOrBr">YlOrBr</option>
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78 <option value="YlOrRd">YlOrRd</option>
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79 <option value="gist_gray">gist_gray</option>
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80 <option value="gist_stern">gist_stern</option>
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81 <option value="gist_earth">gist_earth</option>
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82 <option value="gist_yarg">gist_yarg</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
83 <option value="gist_ncar">gist_ncar</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
84 <option value="gist_rainbow">gist_rainbow</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
85 <option value="gist_heat">gist_heat</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
86 <option value="gnuplot">gnuplot</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
87 <option value="gnuplot2">gnuplot2</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
88 <option value="CMRmap">CMRmap</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
89 <option value="bwr">bwr</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
90 <option value="hsv">hsv</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
91 <option value="brg">brg</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
92 <option value="jet">jet</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
93 <option value="afmhot">afmhot</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
94 <option value="Accent_r">Accent reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
95 <option value="Spectral_r">Spectral reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
96 <option value="Set1_r">Set1 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
97 <option value="Set2_r">Set2 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
98 <option value="Set3_r">Set3 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
99 <option value="Dark2_r">Dark2 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
100 <option value="Reds_r">Reds reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
101 <option value="Oranges_r">Oranges reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
102 <option value="Greens_r">Greens reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
103 <option value="Blues_r">Blues reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
104 <option value="Greys_r">Greys reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
105 <option value="Purples_r">Purples reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
106 <option value="Paired_r">Paired reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
107 <option value="Pastel1_r">Pastel1 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
108 <option value="Pastel2_r">Pastel2 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
109 <option value="spring_r">spring reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
110 <option value="summer_r">summer reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
111 <option value="autumn_r">autumn reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
112 <option value="winter_r">winter reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
113 <option value="hot_r">hot reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
114 <option value="coolwarm_r">coolwarm reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
115 <option value="cool_r">cool reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
116 <option value="seismic_r">seismic reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
117 <option value="terrain_r">terrain reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
118 <option value="ocean_r">ocean reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
119 <option value="rainbow_r">rainbow reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
120 <option value="bone_r">bone reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
121 <option value="flag_r">flag reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
122 <option value="prism_r">prism reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
123 <option value="cubehelix_r">cubehelix reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
124 <option value="binary_r">binary reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
125 <option value="pink_r">pink reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
126 <option value="gray_r">gray reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
127 <option value="copper_r">copper reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
128 <option value="BrBG_r">BrBG reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
129 <option value="BuGn_r">BuGn reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
130 <option value="BuPu_r">BuPu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
131 <option value="GnBu_r">GnBu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
132 <option value="OrRd_r">OrRd reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
133 <option value="PiYG_r">PiYG reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
134 <option value="PRGn_r">PRGn reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
135 <option value="PuOr_r">PuOr reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
136 <option value="PuRd_r">PuRd reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
137 <option value="PuBu_r">PuBu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
138 <option value="RdBu_r">RdBu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
139 <option value="RdGy_r">RdGy reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
140 <option value="RdPu_r">RdPu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
141 <option value="YlGn_r">YlGn reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
142 <option value="PuBuGn_r">PuBuGn reversed</option>
1
8116270ba934 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents: 0
diff changeset
143 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
144 <option value="RdYlGn_r">RdYlGn reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
145 <option value="YlGnBu_r">YlGnBu reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
146 <option value="YlOrBr_r">YlOrBr reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
147 <option value="YlOrRd_r">YlOrRd reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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148 <option value="gist_gray_r">gist_gray reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
149 <option value="gist_stern_r">gist_stern reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
diff changeset
150 <option value="gist_earth_r">gist_earth reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
151 <option value="gist_yarg_r">gist_yarg reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
152 <option value="gist_ncar_r">gist_ncar reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
153 <option value="gist_rainbow_r">gist_rainbow reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
154 <option value="gist_heat_r">gist_heat reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
155 <option value="gnuplot_r">gnuplot reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
156 <option value="gnuplot2_r">gnuplot2 reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
157 <option value="CMRmap_r">CMRmap reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
158 <option value="bwr_r">bwr reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
159 <option value="hsv_r">hsv reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
160 <option value="brg_r">brg reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
parents:
diff changeset
161 <option value="jet_r">jet reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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162 <option value="afmhot_r">afmhot reversed</option>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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parents:
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163 </param>
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164 </xml>
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165
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166
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167 <xml name="multiple_input_matrices">
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168 <repeat name="input_files" title="HiC Matrix files" min="2">
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169 <param name="matrix" type="data" format="h5"
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170 label="HiC Matrix file"
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171 help=""/>
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172 <param name="mlabel" type="text" size="30" optional="true" value=""
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173 label="Label"
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174 help="Label to use in the output. If not given the dataset name will be used instead."/>
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175 </repeat>
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176 </xml>
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177
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178 <token name="@multiple_input_matrices@">
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179 #set $matrices = []
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180 #set $mlabels = []
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181 #for $counter, $i in enumerate($input_files):
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182 ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
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183 #silent $matrices.append( '%s.npz.h5' % $counter )
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184
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185 #if str($i.mlabel.value) != "":
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186 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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187 #else
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188 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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189 #end if
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190 #end for
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191 #set $mlabels = ' '.join($mlabels)
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192 #set $matrices = ' '.join($matrices)
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193 </token>
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194
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195
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196 <xml name="region">
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197 <param name="region" type="text" label="Region of the genome to limit the operation"
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198 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
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199 </xml>
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200
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201
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202
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203 <xml name="kmeans_clustering">
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204 <conditional name="used_multiple_regions">
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205 <param name="used_multiple_regions_options" type="select"
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206 label="Did you compute the matrix with more than one groups of regions?"
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207 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
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208 <option value="yes">Yes, I used multiple groups of regions</option>
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209 <option value="no">No, I used only one group</option>
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210 </param>
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211 <when value="no">
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212 <conditional name="clustering">
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213 <param name="clustering_options" type="select" label="Clustering algorithm">
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214 <option value="none">No clustering</option>
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215 <option value="kmeans">Kmeans clustering</option>
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216 </param>
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217 <when value="kmeans">
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218 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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219 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
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220 </when>
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221 <when value="none" />
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222 </conditional>
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223 </when>
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224 <when value="yes" />
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225 </conditional>
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226 </xml>
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227
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228 <token name="@KMEANS_CLUSTERING@">
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229 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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230 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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231 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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232 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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233 #end if
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234 #end if
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235 #end if
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236 </token>
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237
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238 <xml name="samFlag">
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239 <param name="samFlag" type="integer" optional="true" value=""
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240 label="Filter reads based on the SAM flag"
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241 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
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242 </xml>
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243 <xml name="plotNumbers">
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244 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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245 label="Plot the correlation value"
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246 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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247 </xml>
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248 <xml name="doNotExtendPairedEnds">
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249 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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250 label="Do not extend paired ends"
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251 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
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252 </xml>
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253
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254 <xml name="ignoreDuplicates">
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255 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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256 label="Ignore duplicates"
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257 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
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258 </xml>
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259
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260 <xml name="minMappingQuality">
1
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261 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
0
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262 label="Minimum mapping quality"
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263 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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264 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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265 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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266 </xml>
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267
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268 <xml name="skipZeros">
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269 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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270 label ="Skip zeros"
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271 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
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272 </xml>
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273
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274 <xml name="fragmentLength">
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275 <param name="fragmentLength" type="integer" value="300" min="1"
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276 label="Fragment length used for the sequencing"
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277 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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278 </xml>
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279
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280 <xml name="scaleFactor">
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281 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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282 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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283 </xml>
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284
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285 <xml name="xMax">
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286 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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287 label="Max value for the x-axis in counts per bin" />
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288 </xml>
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289
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290 <xml name="filterThreshold">
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291 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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292 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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293
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294 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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295 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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296 </xml>
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297
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298
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299 <xml name="pseudocount">
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300 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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301 </xml>
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302
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303 <token name="@REFERENCES@">
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304
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305 .. class:: infomark
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306
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307 For more information on the tools, please visit our `help site`_.
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308
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309 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
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310
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311 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
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312
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313 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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314 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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315 .. _help site: https://hicexplorer.readthedocs.org
0
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316
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317 </token>
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318
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319
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320 <xml name="multiple_input_bams">
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321 <repeat name="input_files" title="BAM files" min="2">
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322 <param name="bamfile" type="data" format="bam"
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323 label="Bam file"
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324 help="The BAM file must be sorted."/>
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325 <param name="label" type="text" size="30" optional="true" value=""
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326 label="Label"
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327 help="Label to use in the output. If not given the dataset name will be used instead."/>
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328 </repeat>
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329 </xml>
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330
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331 <xml name="multiple_input_bigwigs">
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332 <repeat name="input_files" title="BigWig files" min="2">
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333 <param name="bigwigfile" type="data" format="bigwig"
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334 label="Bigwig file"
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335 help="The Bigwig file must be sorted."/>
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336 <param name="label" type="text" size="30" optional="true" value=""
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337 label="Label"
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338 help="Label to use in the output. If not given the dataset name will be used instead."/>
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339 </repeat>
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340 </xml>
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341
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342 <xml name="plotTitle">
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343 <param name="plotTitle" type="text" value="" size="30" optional="True"
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344 label="Title of the plot"
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345 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
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346 </xml>
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347
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348 <token name="@multiple_input_bams@">
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349 #import tempfile
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350 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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351 #set files=[]
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352 #set labels=[]
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353 #for $i in $input_files:
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354 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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355 #set $temp_input_path = $temp_input_handle.name
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356 #silent $temp_input_handle.close()
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357 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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358 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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359 #silent $files.append('%s.bam' % $temp_input_path)
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360
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361 ##set $files += [str($i.bamfile)]
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362 #if str($i.label.value) != "":
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363 #set $labels += ["\"%s\"" % ($i.label.value)]
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364 #else
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365 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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366 #end if
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367 #end for
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368 </token>
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369
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370 <token name="@multiple_input_bigwigs@">
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371 #import tempfile
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372 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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373 #set files=[]
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374 #set labels=[]
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375 #for $i in $input_files:
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376 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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377 #set $temp_input_path = $temp_input_handle.name
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378 #silent $temp_input_handle.close()
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379 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
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380 #silent $files.append('%s.bw' % $temp_input_path)
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381
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382 ##set $files += [str($i.bigwigfile)]
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383 #if str($i.label.value) != "":
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384 #set $labels += ["\"%s\"" % ($i.label.value)]
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385 #else
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386 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
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387 #end if
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388 #end for
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389 </token>
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390
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391 <xml name="reference_genome_source">
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392 <conditional name="source">
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393 <param name="ref_source" type="select" label="Reference genome">
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394 <option value="cached">locally cached</option>
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395 <option value="history">in your history</option>
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396 </param>
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397 <when value="cached">
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398 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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399 <options from_data_table="deepTools_seqs">
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400 <filter type="sort_by" column="1" />
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401 <validator type="no_options" message="No indexes are available." />
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402 </options>
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403 </param>
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404 </when>
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405 <when value="history">
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406 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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407 </when>
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408 </conditional>
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409 </xml>
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410
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411 <token name="@reference_genome_source@">
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412 #if $source.ref_source=="history":
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413 --genome $source.input1
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414 #else:
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415 --genome "${source.input1_2bit.fields.path}"
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416 #end if
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417 </token>
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418
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419 <xml name="effectiveGenomeSize">
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420 <conditional name="effectiveGenomeSize">
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421 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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422 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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423 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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424 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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425 <option value="93260000">ce10 (93260000)</option>
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426 <option value="121400000">dm3 (121400000)</option>
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427 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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428 <option value="2150570000">mm9 (2150570000)</option>
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429 <option value="specific">user specified</option>
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430 </param>
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431 <when value="specific">
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432 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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433 </when>
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434 <when value="2150570000" />
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435 <when value="2451960000" />
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436 <when value="121400000" />
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437 <when value="93260000" />
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438 </conditional>
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439 </xml>
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440
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441 <xml name="image_file_format">
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442 <param name="outFileFormat" type="select" label="Image file format">
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443 <option value="png" selected="true">png</option>
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444 <option value="pdf">pdf</option>
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445 <option value="svg">svg</option>
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446 <option value="eps">eps</option>
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447 <option value="emf">emf</option>
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448 </param>
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449 </xml>
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450
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451 <xml name="missingDataAsZero">
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452 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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453 label ="Treat missing data as zero"
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454 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
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455 </xml>
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456
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457 <xml name="input_save_matrix_values">
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458 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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459 </xml>
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460
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461 <xml name="input_graphic_output_settings">
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462 <conditional name="output" >
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463 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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464 <option value="no" selected="true">no</option>
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465 <option value="yes">yes</option>
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466 </param>
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467 <when value="no" />
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468 <when value="yes">
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469 <yield />
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470 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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471 <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."/>
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472 </when>
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473 </conditional>
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474 </xml>
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475
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476 <xml name="input_image_file_format">
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477 <param name="outFileFormat" type="select" label="Image file format">
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478 <option value="png" selected="true">png</option>
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479 <option value="pdf">pdf</option>
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480 <option value="svg">svg</option>
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481 <option value="eps">eps</option>
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482 <option value="emf">emf</option>
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483 </param>
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484 </xml>
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485
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486 <xml name="output_image_file_format">
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487 <data format="png" name="outFileName" label="${tool.name} image">
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488 <change_format>
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489 <when input="output.outFileFormat" value="pdf" format="pdf" />
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490 <when input="output.outFileFormat" value="svg" format="svg" />
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491 <when input="output.outFileFormat" value="eps" format="eps" />
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492 <when input="output.outFileFormat" value="emf" format="emf" />
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493 </change_format>
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494 </data>
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495 </xml>
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496
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497 <xml name="output_save_matrix_values">
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498 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
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499 <filter>
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500 ((
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501 output['showOutputSettings'] == 'yes' and
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502 output['saveMatrix'] is True
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503 ))
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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504 </filter>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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505 </data>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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506 </xml>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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507
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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508 <xml name="output_graphic_outputs">
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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509 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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510 <filter>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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511 ((
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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512 output['showOutputSettings'] == 'yes' and
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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513 output['saveData'] is True
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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514 ))
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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515 </filter>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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516 </data>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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517 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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518 <filter>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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519 ((
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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520 output['showOutputSettings'] == 'yes' and
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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521 output['saveSortedRegions'] is True
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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522 ))
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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523 </filter>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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524 </data>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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525 </xml>
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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526
3
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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527 <xml name="track_input_h5_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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528 <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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529 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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530 <xml name="track_input_bed_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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531 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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532 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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533 <xml name="track_input_bedgraph_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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534 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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535 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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536 <xml name="track_input_bigwig_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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537 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
diff changeset
538 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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539 <xml name="track_input_bedgraph_matrix_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
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540 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
diff changeset
541 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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542 <xml name="track_input_tabular_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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543 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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544 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
diff changeset
545 <xml name="plot_title">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
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546 <param name="title" type="text" optional="true" label="Plot title"/>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
547 </xml>
0
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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548
3
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
549 <xml name="spacer_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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550 <param name="spacer_width" type="float" value="" optional="True"
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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551 label="Include spacer at the end of the track." help="Width of the spacer." />
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
552 </xml>
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
diff changeset
553 <xml name="fontsize_macro">
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
parents: 2
diff changeset
554 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
7c2c17b2c4a6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 2
diff changeset
555 </xml>
0
70cdd1d37637 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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556 </macros>