Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

annotate macros.xml.orig @ 9:e1e5b2c47c00 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
author iuc
date Wed, 07 Mar 2018 02:27:16 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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3 <<<<<<< HEAD
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4 <token name="@WRAPPER_VERSION@">2.0</token>
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5
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6 <token name="@USE_RANGE@">
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7 #if $use_range.select_use_range == "yes_use_range":
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8 --range $range_min:$range_max
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9 #end if
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10 </token>
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11
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12 =======
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13 <token name="@WRAPPER_VERSION@">2.1alpha1</token>
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14 >>>>>>> joachimwolff-master
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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18 <yield />
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19 </requirements>
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20 <version_command>@BINARY@ --version</version_command>
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21 </xml>
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22
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23 <xml name="citations">
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24 <citations>
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25 <citation type="doi">10.5281/zenodo.1133705</citation>
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26 <yield />
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27 </citations>
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28 </xml>
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29
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30 <xml name="zMax">
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31 <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 -->
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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32 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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33 <xml name="use_range">
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34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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35 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
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36 <option value="no_use_range">No restriction</option>
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37 <option value="yes_use_range">Only consider counts within a range</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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38 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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39 <when value="no_use_range"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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40 <when value="yes_use_range">
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41 <param name="range_min" type="integer" value="" min="0"/>
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42 <param name="range_max" type="integer" value="" min="0"/>
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43 </when>
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44 </conditional>
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45 </xml>
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46 <xml name="colormap">
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47 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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48 <option value="RdYlBu">RdYlBu</option>
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49 <option value="Accent">Accent</option>
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50 <option value="Spectral">Spectral</option>
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51 <option value="Set1">Set1</option>
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52 <option value="Set2">Set2</option>
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53 <option value="Set3">Set3</option>
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54 <option value="Dark2">Dark2</option>
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55 <option value="Reds">Reds</option>
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56 <option value="Oranges">Oranges</option>
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57 <option value="Greens">Greens</option>
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58 <option value="Blues">Blues</option>
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59 <option value="Greys">Greys</option>
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60 <option value="Purples">Purples</option>
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61 <option value="Paired">Paired</option>
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62 <option value="Pastel1">Pastel1</option>
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63 <option value="Pastel2">Pastel2</option>
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64 <option value="spring">spring</option>
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65 <option value="summer">summer</option>
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66 <option value="autumn">autumn</option>
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67 <option value="winter">winter</option>
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68 <option value="hot">hot</option>
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69 <option value="coolwarm">coolwarm</option>
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70 <option value="cool">cool</option>
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71 <option value="seismic">seismic</option>
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72 <option value="terrain">terrain</option>
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73 <option value="ocean">ocean</option>
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74 <option value="rainbow">rainbow</option>
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75 <option value="bone">bone</option>
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76 <option value="flag">flag</option>
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77 <option value="prism">prism</option>
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78 <option value="cubehelix">cubehelix</option>
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79 <option value="binary">binary</option>
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80 <option value="pink">pink</option>
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81 <option value="gray">gray</option>
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82 <option value="copper">copper</option>
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83 <option value="BrBG">BrBG</option>
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84 <option value="BuGn">BuGn</option>
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iuc
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diff changeset
85 <option value="BuPu">BuPu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
86 <option value="GnBu">GnBu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
87 <option value="OrRd">OrRd</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
88 <option value="PiYG">PiYG</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
89 <option value="PRGn">PRGn</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
90 <option value="PuOr">PuOr</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
91 <option value="PuRd">PuRd</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
92 <option value="PuBu">PuBu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
93 <option value="RdBu">RdBu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
94 <option value="RdGy">RdGy</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
95 <option value="RdPu">RdPu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
96 <option value="YlGn">YlGn</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
97 <option value="PuBuGn">PuBuGn</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
98 <option value="RdYlGn">RdYlGn</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
99 <option value="YlGnBu">YlGnBu</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
100 <option value="YlOrBr">YlOrBr</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
101 <option value="YlOrRd">YlOrRd</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
102 <option value="gist_gray">gist_gray</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
103 <option value="gist_stern">gist_stern</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
104 <option value="gist_earth">gist_earth</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
105 <option value="gist_yarg">gist_yarg</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
106 <option value="gist_ncar">gist_ncar</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
107 <option value="gist_rainbow">gist_rainbow</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
108 <option value="gist_heat">gist_heat</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
109 <option value="gnuplot">gnuplot</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
110 <option value="gnuplot2">gnuplot2</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
111 <option value="CMRmap">CMRmap</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
112 <option value="bwr">bwr</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
113 <option value="hsv">hsv</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
114 <option value="brg">brg</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
115 <option value="jet">jet</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
116 <option value="afmhot">afmhot</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
117 <option value="Accent_r">Accent reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
118 <option value="Spectral_r">Spectral reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
119 <option value="Set1_r">Set1 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
120 <option value="Set2_r">Set2 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
121 <option value="Set3_r">Set3 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
122 <option value="Dark2_r">Dark2 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
123 <option value="Reds_r">Reds reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
124 <option value="Oranges_r">Oranges reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
125 <option value="Greens_r">Greens reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
126 <option value="Blues_r">Blues reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
127 <option value="Greys_r">Greys reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
128 <option value="Purples_r">Purples reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
129 <option value="Paired_r">Paired reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
130 <option value="Pastel1_r">Pastel1 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
131 <option value="Pastel2_r">Pastel2 reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
132 <option value="spring_r">spring reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
133 <option value="summer_r">summer reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
134 <option value="autumn_r">autumn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
135 <option value="winter_r">winter reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
136 <option value="hot_r">hot reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
137 <option value="coolwarm_r">coolwarm reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
138 <option value="cool_r">cool reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
139 <option value="seismic_r">seismic reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
140 <option value="terrain_r">terrain reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
141 <option value="ocean_r">ocean reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
142 <option value="rainbow_r">rainbow reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
143 <option value="bone_r">bone reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
144 <option value="flag_r">flag reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
145 <option value="prism_r">prism reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
146 <option value="cubehelix_r">cubehelix reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
147 <option value="binary_r">binary reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
148 <option value="pink_r">pink reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
149 <option value="gray_r">gray reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
150 <option value="copper_r">copper reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
151 <option value="BrBG_r">BrBG reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
152 <option value="BuGn_r">BuGn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
153 <option value="BuPu_r">BuPu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
154 <option value="GnBu_r">GnBu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
155 <option value="OrRd_r">OrRd reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
156 <option value="PiYG_r">PiYG reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
157 <option value="PRGn_r">PRGn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
158 <option value="PuOr_r">PuOr reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
159 <option value="PuRd_r">PuRd reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
160 <option value="PuBu_r">PuBu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
161 <option value="RdBu_r">RdBu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
162 <option value="RdGy_r">RdGy reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
163 <option value="RdPu_r">RdPu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
164 <option value="YlGn_r">YlGn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
165 <option value="PuBuGn_r">PuBuGn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
167 <option value="RdYlGn_r">RdYlGn reversed</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
168 <option value="YlGnBu_r">YlGnBu reversed</option>
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169 <option value="YlOrBr_r">YlOrBr reversed</option>
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170 <option value="YlOrRd_r">YlOrRd reversed</option>
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171 <option value="gist_gray_r">gist_gray reversed</option>
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172 <option value="gist_stern_r">gist_stern reversed</option>
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173 <option value="gist_earth_r">gist_earth reversed</option>
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174 <option value="gist_yarg_r">gist_yarg reversed</option>
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175 <option value="gist_ncar_r">gist_ncar reversed</option>
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176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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177 <option value="gist_heat_r">gist_heat reversed</option>
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178 <option value="gnuplot_r">gnuplot reversed</option>
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179 <option value="gnuplot2_r">gnuplot2 reversed</option>
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180 <option value="CMRmap_r">CMRmap reversed</option>
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181 <option value="bwr_r">bwr reversed</option>
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182 <option value="hsv_r">hsv reversed</option>
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183 <option value="brg_r">brg reversed</option>
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184 <option value="jet_r">jet reversed</option>
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185 <option value="afmhot_r">afmhot reversed</option>
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186 </param>
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187 </xml>
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188
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189
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190 <xml name="multiple_input_matrices">
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191 <repeat name="input_files" title="HiC Matrix files" min="2">
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192 <param name="matrix" type="data" format="h5,cool"
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193 label="HiC Matrix file"
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194 help=""/>
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195 <param name="mlabel" type="text" size="30" optional="true" value=""
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196 label="Label"
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197 help="Label to use in the output. If not given the dataset name will be used instead."/>
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198 </repeat>
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199 </xml>
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200
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201 <token name="@multiple_input_matrices@">
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202 #set $matrices = []
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203 #set $mlabels = []
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204 #for $counter, $i in enumerate($input_files):
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205 ln -s $i.matrix #echo str($counter)+'_matrix'#;
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206 #silent $matrices.append( '%s_matrix' % $counter )
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207
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208 #if str($i.mlabel.value) != "":
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209 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
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210 #else
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211 #set $mlabels += ['"%s"' % ($i.matrix.name)]
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212 #end if
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213 #end for
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214 #set $mlabels = ' '.join($mlabels)
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215 #set $matrices = ' '.join($matrices)
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216 </token>
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217
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218
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219 <xml name="region">
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220 <param name="region" type="text" label="Region of the genome to limit the operation"
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221 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" argument="--region"/>
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222 </xml>
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223
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224
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225
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226 <xml name="kmeans_clustering">
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227 <conditional name="used_multiple_regions">
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228 <param name="used_multiple_regions_options" type="select"
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229 label="Did you compute the matrix with more than one groups of regions?"
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230 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
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231 <option value="yes">Yes, I used multiple groups of regions</option>
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232 <option value="no">No, I used only one group</option>
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233 </param>
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234 <when value="no">
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235 <conditional name="clustering">
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236 <param name="clustering_options" type="select" label="Clustering algorithm">
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237 <option value="none">No clustering</option>
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238 <option value="kmeans">Kmeans clustering</option>
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239 </param>
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240 <when value="kmeans">
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241 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
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242 help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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243 </when>
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244 <when value="none" />
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245 </conditional>
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246 </when>
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247 <when value="yes" />
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248 </conditional>
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249 </xml>
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250
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251 <token name="@KMEANS_CLUSTERING@">
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252 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
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253 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
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254 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
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255 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
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256 #end if
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257 #end if
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258 #end if
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259 </token>
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260
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261 <xml name="samFlag">
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262 <param name="samFlag" type="integer" optional="true" value=""
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263 label="Filter reads based on the SAM flag"
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264 help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
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265 </xml>
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266 <xml name="plotNumbers">
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267 <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
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268 label="Plot the correlation value"
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269 help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
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270 </xml>
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271 <xml name="doNotExtendPairedEnds">
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272 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
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273 label="Do not extend paired ends"
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274 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
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275 </xml>
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276
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277 <xml name="ignoreDuplicates">
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278 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
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279 label="Ignore duplicates"
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280 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read. (--ignoreDuplicates)" />
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281 </xml>
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282
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283 <xml name="minMappingQuality">
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284 <param argument="--minMappingQuality" type="integer" optional="true" value="" min="1"
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285 label="Minimum mapping quality"
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286 help= "If set, only reads that have a mapping quality score higher than the given value are considered.
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287 *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read.
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288 A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
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289 </xml>
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290
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291 <xml name="skipZeros">
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292 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
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293 label ="Skip zeros"
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294 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" />
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295 </xml>
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296
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297 <xml name="fragmentLength">
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298 <param name="fragmentLength" type="integer" value="300" min="1"
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299 label="Fragment length used for the sequencing"
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300 help ="If paired-end reads are used, the fragment length is computed from the BAM file. (--fragmentLength)"/>
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301 </xml>
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302
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303 <xml name="scaleFactor">
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304 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
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305 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
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306 </xml>
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307
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308 <xml name="xMax">
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309 <param argument="--xMax" name="xMax" type="integer" optional="true" value=""
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310 label="Max value for the x-axis in counts per bin" />
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311 </xml>
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312
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313 <xml name="filterThreshold">
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314 <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5"
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315 label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect."/>
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316
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317 <param argument="--filterThreshold" name="filterThreshold_large" type="float" value="5.0"
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318 label="Remove bins of large coverage" help="e.g. 5; Both Thresholds needs to be set to take effect."/>
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319 </xml>
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320
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321 <xml name="pseudocount">
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322 <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
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323 </xml>
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324 <xml name='matrix_h5_cooler_macro'>
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325 <param name='matrix_h5_cooler' type="data" format="h5,cool"
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326 label="Matrix to compute on"/>
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327 </xml>
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328 <xml name='matrix_h5_cooler_multiple_macro'>
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329 <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool"
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330 label="Matricies to compute on" multiple="true"/>
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331 </xml>
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332 <token name="@REFERENCES@">
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333
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334 .. class:: infomark
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335
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336 For more information on the tools, please visit our `help site`_.
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337
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338 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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339
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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340 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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341
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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342 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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343 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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344 .. _help site: https://hicexplorer.readthedocs.org
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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345
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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346 </token>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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347
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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348
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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349 <xml name="multiple_input_bams">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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350 <repeat name="input_files" title="BAM files" min="2">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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351 <param name="bamfile" type="data" format="bam"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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352 label="Bam file"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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353 help="The BAM file must be sorted."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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354 <param name="label" type="text" size="30" optional="true" value=""
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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355 label="Label"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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356 help="Label to use in the output. If not given the dataset name will be used instead."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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357 </repeat>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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358 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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359
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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360 <xml name="multiple_input_bigwigs">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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361 <repeat name="input_files" title="BigWig files" min="2">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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362 <param name="bigwigfile" type="data" format="bigwig"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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363 label="Bigwig file"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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364 help="The Bigwig file must be sorted."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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365 <param name="label" type="text" size="30" optional="true" value=""
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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366 label="Label"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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367 help="Label to use in the output. If not given the dataset name will be used instead."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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368 </repeat>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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369 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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370
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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371 <xml name="plotTitle">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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372 <param name="plotTitle" type="text" value="" size="30" optional="True"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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373 label="Title of the plot"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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375 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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376
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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377 <token name="@multiple_input_bams@">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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378 #import tempfile
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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380 #set files=[]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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381 #set labels=[]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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382 #for $i in $input_files:
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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384 #set $temp_input_path = $temp_input_handle.name
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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385 #silent $temp_input_handle.close()
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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388 #silent $files.append('%s.bam' % $temp_input_path)
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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389
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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390 ##set $files += [str($i.bamfile)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
391 #if str($i.label.value) != "":
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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392 #set $labels += ["\"%s\"" % ($i.label.value)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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393 #else
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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394 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
395 #end if
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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396 #end for
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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397 </token>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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398
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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399 <token name="@multiple_input_bigwigs@">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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400 #import tempfile
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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402 #set files=[]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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403 #set labels=[]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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404 #for $i in $input_files:
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
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406 #set $temp_input_path = $temp_input_handle.name
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
407 #silent $temp_input_handle.close()
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
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diff changeset
408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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409 #silent $files.append('%s.bw' % $temp_input_path)
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
410
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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411 ##set $files += [str($i.bigwigfile)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
412 #if str($i.label.value) != "":
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
413 #set $labels += ["\"%s\"" % ($i.label.value)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
414 #else
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
416 #end if
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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417 #end for
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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418 </token>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
419
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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420 <xml name="reference_genome_source">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
421 <conditional name="source">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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422 <param name="ref_source" type="select" label="Reference genome">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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423 <option value="cached">locally cached</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
424 <option value="history">in your history</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
425 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
426 <when value="cached">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
427 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
428 <options from_data_table="deepTools_seqs">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
429 <filter type="sort_by" column="1" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
diff changeset
430 <validator type="no_options" message="No indexes are available." />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
431 </options>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
432 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
433 </when>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
434 <when value="history">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
436 </when>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
437 </conditional>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
438 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
439
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
440 <token name="@reference_genome_source@">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
441 #if $source.ref_source=="history":
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
442 --genome $source.input1
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
443 #else:
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
444 --genome "${source.input1_2bit.fields.path}"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
445 #end if
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
446 </token>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
447
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
448 <xml name="effectiveGenomeSize">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
449 <conditional name="effectiveGenomeSize">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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451 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.
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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453 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.">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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454 <option value="93260000">ce10 (93260000)</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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455 <option value="121400000">dm3 (121400000)</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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456 <option value="2451960000" selected="true">hg19 (2451960000)</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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457 <option value="2150570000">mm9 (2150570000)</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
458 <option value="specific">user specified</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
459 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
460 <when value="specific">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
462 </when>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
463 <when value="2150570000" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
464 <when value="2451960000" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
465 <when value="121400000" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
466 <when value="93260000" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
467 </conditional>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
468 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
469
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
470 <xml name="image_file_format">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
471 <param name="outFileFormat" type="select" label="Image file format">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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472 <option value="png" selected="true">png</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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473 <option value="pdf">pdf</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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474 <option value="svg">svg</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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475 <option value="eps">eps</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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476 <option value="emf">emf</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
477 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
478 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
479
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
480 <xml name="missingDataAsZero">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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482 label ="Treat missing data as zero"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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483 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." />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
484 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
485
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
486 <xml name="input_save_matrix_values">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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488 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
489
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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490 <xml name="input_graphic_output_settings">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
491 <conditional name="output" >
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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492 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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493 <option value="no" selected="true">no</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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494 <option value="yes">yes</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
495 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
496 <when value="no" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
497 <when value="yes">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
498 <yield />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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500 <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."/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
501 </when>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
502 </conditional>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
503 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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diff changeset
504
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
diff changeset
505 <xml name="input_image_file_format">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
diff changeset
506 <param name="outFileFormat" type="select" label="Image file format">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
diff changeset
507 <option value="png" selected="true">png</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
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508 <option value="pdf">pdf</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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parents:
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509 <option value="svg">svg</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
510 <option value="eps">eps</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
511 <option value="emf">emf</option>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
512 </param>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
513 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
514
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
515 <xml name="output_image_file_format">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
516 <data format="png" name="outFileName" label="${tool.name} image">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
517 <change_format>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
518 <when input="output.outFileFormat" value="pdf" format="pdf" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
519 <when input="output.outFileFormat" value="svg" format="svg" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
520 <when input="output.outFileFormat" value="eps" format="eps" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
521 <when input="output.outFileFormat" value="emf" format="emf" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
522 </change_format>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
523 </data>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
524 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
525
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
526 <xml name="output_save_matrix_values">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
527 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
528 <filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
529 ((
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
530 output['showOutputSettings'] == 'yes' and
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
531 output['saveMatrix'] is True
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
532 ))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
533 </filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
534 </data>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
535 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
536
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
537 <xml name="output_graphic_outputs">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
538 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
539 <filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
540 ((
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
541 output['showOutputSettings'] == 'yes' and
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
542 output['saveData'] is True
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
543 ))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
544 </filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
545 </data>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
547 <filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
548 ((
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
549 output['showOutputSettings'] == 'yes' and
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
550 output['saveSortedRegions'] is True
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
551 ))
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
552 </filter>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
553 </data>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
554 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
555
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
556 <xml name="track_input_h5_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
557 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
558 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
559 <xml name="track_input_bed_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
560 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
561 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
562 <xml name="track_input_bedgraph_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
563 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
564 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
565 <xml name="track_input_bigwig_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
566 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
567 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
568 <xml name="track_input_bedgraph_matrix_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
569 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
570 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
571 <xml name="track_input_tabular_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
572 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
573 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
574 <xml name="plot_title">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
575 <param name="title" type="text" optional="true" label="Plot title"/>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
576 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
577
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
578 <xml name="spacer_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
579 <param name="spacer_width" type="float" value="" optional="True"
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
580 label="Include spacer at the end of the track." help="Width of the spacer." />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
581 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
582 <xml name="fontsize_macro">
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
583 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
584 </xml>
e1e5b2c47c00 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
585 </macros>