Mercurial > repos > bgruening > hicexplorer_hicsummatrices

annotate macros.xml @ 3:81d637d11316 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author iuc
date Thu, 02 Nov 2017 10:53:43 -0400
parents 02aa5e8bc7be
children 56dda810d0c2
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1 <macros>
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
iuc
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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3 <token name="@WRAPPER_VERSION@">1.8</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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11
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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/">
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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>
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83 <option value="gist_ncar">gist_ncar</option>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e 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>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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106 <option value="Paired_r">Paired reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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107 <option value="Pastel1_r">Pastel1 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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108 <option value="Pastel2_r">Pastel2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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109 <option value="spring_r">spring reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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110 <option value="summer_r">summer reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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111 <option value="autumn_r">autumn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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112 <option value="winter_r">winter reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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113 <option value="hot_r">hot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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114 <option value="coolwarm_r">coolwarm reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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115 <option value="cool_r">cool reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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116 <option value="seismic_r">seismic reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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117 <option value="terrain_r">terrain reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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118 <option value="ocean_r">ocean reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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119 <option value="rainbow_r">rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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120 <option value="bone_r">bone reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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121 <option value="flag_r">flag reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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122 <option value="prism_r">prism reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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123 <option value="cubehelix_r">cubehelix reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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124 <option value="binary_r">binary reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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125 <option value="pink_r">pink reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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126 <option value="gray_r">gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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127 <option value="copper_r">copper reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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128 <option value="BrBG_r">BrBG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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129 <option value="BuGn_r">BuGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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130 <option value="BuPu_r">BuPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
bgruening
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131 <option value="GnBu_r">GnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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132 <option value="OrRd_r">OrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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133 <option value="PiYG_r">PiYG reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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134 <option value="PRGn_r">PRGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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135 <option value="PuOr_r">PuOr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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136 <option value="PuRd_r">PuRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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137 <option value="PuBu_r">PuBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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138 <option value="RdBu_r">RdBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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139 <option value="RdGy_r">RdGy reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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140 <option value="RdPu_r">RdPu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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141 <option value="YlGn_r">YlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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142 <option value="PuBuGn_r">PuBuGn reversed</option>
1
a6ccec9faaa3 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
143 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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144 <option value="RdYlGn_r">RdYlGn reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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145 <option value="YlGnBu_r">YlGnBu reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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146 <option value="YlOrBr_r">YlOrBr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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147 <option value="YlOrRd_r">YlOrRd reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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148 <option value="gist_gray_r">gist_gray reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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149 <option value="gist_stern_r">gist_stern reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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150 <option value="gist_earth_r">gist_earth reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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151 <option value="gist_yarg_r">gist_yarg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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152 <option value="gist_ncar_r">gist_ncar reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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153 <option value="gist_rainbow_r">gist_rainbow reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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154 <option value="gist_heat_r">gist_heat reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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155 <option value="gnuplot_r">gnuplot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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156 <option value="gnuplot2_r">gnuplot2 reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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157 <option value="CMRmap_r">CMRmap reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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158 <option value="bwr_r">bwr reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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159 <option value="hsv_r">hsv reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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160 <option value="brg_r">brg reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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161 <option value="jet_r">jet reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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162 <option value="afmhot_r">afmhot reversed</option>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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163 </param>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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164 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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165
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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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 )
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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 ${on_string}: Heatmap values">
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499 <filter>
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500 ((
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501 output['showOutputSettings'] == 'yes' and
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502 output['saveMatrix'] is True
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503 ))
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504 </filter>
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505 </data>
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506 </xml>
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507
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508 <xml name="output_graphic_outputs">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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509 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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510 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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511 ((
f638ffde832e 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
f638ffde832e 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
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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514 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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515 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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516 </data>
f638ffde832e 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">
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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518 <filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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519 ((
f638ffde832e 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
f638ffde832e 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
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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522 ))
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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523 </filter>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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524 </data>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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525 </xml>
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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526
3
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527 <xml name="track_input_h5_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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528 <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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529 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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530 <xml name="track_input_bed_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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531 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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532 </xml>
81d637d11316 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">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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534 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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535 </xml>
81d637d11316 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">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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537 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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539 <xml name="track_input_bedgraph_matrix_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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540 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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541 </xml>
81d637d11316 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">
81d637d11316 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"/>
81d637d11316 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>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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545 <xml name="plot_title">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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546 <param name="title" type="text" optional="true" label="Plot title"/>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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547 </xml>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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548
3
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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549 <xml name="spacer_macro">
81d637d11316 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"
81d637d11316 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." />
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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552 </xml>
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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553 <xml name="fontsize_macro">
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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554 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
81d637d11316 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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555 </xml>
0
f638ffde832e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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556 </macros>