Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

annotate macros.xml.orig @ 9:79d10df2108e 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 02:18:44 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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1 <macros>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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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 -->
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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32 </xml>
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33 <xml name="use_range">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
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34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
79d10df2108e 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>
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38 </param>
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39 <when value="no_use_range"/>
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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">
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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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85 <option value="BuPu">BuPu</option>
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86 <option value="GnBu">GnBu</option>
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diff changeset
87 <option value="OrRd">OrRd</option>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
169 <option value="YlOrBr_r">YlOrBr reversed</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
170 <option value="YlOrRd_r">YlOrRd reversed</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
171 <option value="gist_gray_r">gist_gray reversed</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
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)."/>
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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
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339
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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`_.
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341
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342 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
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343 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
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344 .. _help site: https://hicexplorer.readthedocs.org
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345
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346 </token>
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347
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348
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
349 <xml name="multiple_input_bams">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
350 <repeat name="input_files" title="BAM files" min="2">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
351 <param name="bamfile" type="data" format="bam"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
352 label="Bam file"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
353 help="The BAM file must be sorted."/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
354 <param name="label" type="text" size="30" optional="true" value=""
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
355 label="Label"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
356 help="Label to use in the output. If not given the dataset name will be used instead."/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
357 </repeat>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
358 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
359
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
360 <xml name="multiple_input_bigwigs">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
361 <repeat name="input_files" title="BigWig files" min="2">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
362 <param name="bigwigfile" type="data" format="bigwig"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
363 label="Bigwig file"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
364 help="The Bigwig file must be sorted."/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
365 <param name="label" type="text" size="30" optional="true" value=""
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
366 label="Label"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
367 help="Label to use in the output. If not given the dataset name will be used instead."/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
368 </repeat>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
369 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
370
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
371 <xml name="plotTitle">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
372 <param name="plotTitle" type="text" value="" size="30" optional="True"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
373 label="Title of the plot"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
375 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
376
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
377 <token name="@multiple_input_bams@">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
378 #import tempfile
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
380 #set files=[]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
381 #set labels=[]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
382 #for $i in $input_files:
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
384 #set $temp_input_path = $temp_input_handle.name
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
385 #silent $temp_input_handle.close()
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
388 #silent $files.append('%s.bam' % $temp_input_path)
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
389
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
390 ##set $files += [str($i.bamfile)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
391 #if str($i.label.value) != "":
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
392 #set $labels += ["\"%s\"" % ($i.label.value)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
393 #else
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
394 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
395 #end if
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
396 #end for
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
397 </token>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
398
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
399 <token name="@multiple_input_bigwigs@">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
400 #import tempfile
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
402 #set files=[]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
403 #set labels=[]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
404 #for $i in $input_files:
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
406 #set $temp_input_path = $temp_input_handle.name
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
407 #silent $temp_input_handle.close()
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
409 #silent $files.append('%s.bw' % $temp_input_path)
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
410
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
411 ##set $files += [str($i.bigwigfile)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
412 #if str($i.label.value) != "":
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
413 #set $labels += ["\"%s\"" % ($i.label.value)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
414 #else
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
416 #end if
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
417 #end for
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
418 </token>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
419
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
420 <xml name="reference_genome_source">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
421 <conditional name="source">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
422 <param name="ref_source" type="select" label="Reference genome">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
423 <option value="cached">locally cached</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
424 <option value="history">in your history</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
425 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
426 <when value="cached">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
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">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
428 <options from_data_table="deepTools_seqs">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
429 <filter type="sort_by" column="1" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
430 <validator type="no_options" message="No indexes are available." />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
431 </options>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
432 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
433 </when>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
434 <when value="history">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
436 </when>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
437 </conditional>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
438 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
439
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
440 <token name="@reference_genome_source@">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
441 #if $source.ref_source=="history":
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
442 --genome $source.input1
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
443 #else:
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
444 --genome "${source.input1_2bit.fields.path}"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
445 #end if
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
446 </token>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
447
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
448 <xml name="effectiveGenomeSize">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
449 <conditional name="effectiveGenomeSize">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
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.
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
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.">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
454 <option value="93260000">ce10 (93260000)</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
455 <option value="121400000">dm3 (121400000)</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
456 <option value="2451960000" selected="true">hg19 (2451960000)</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
457 <option value="2150570000">mm9 (2150570000)</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
458 <option value="specific">user specified</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
459 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
460 <when value="specific">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
462 </when>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
463 <when value="2150570000" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
464 <when value="2451960000" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
465 <when value="121400000" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
466 <when value="93260000" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
467 </conditional>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
468 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
469
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
470 <xml name="image_file_format">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
471 <param name="outFileFormat" type="select" label="Image file format">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
472 <option value="png" selected="true">png</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
473 <option value="pdf">pdf</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
474 <option value="svg">svg</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
475 <option value="eps">eps</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
476 <option value="emf">emf</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
477 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
478 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
479
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
480 <xml name="missingDataAsZero">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
482 label ="Treat missing data as zero"
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
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." />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
484 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
485
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
486 <xml name="input_save_matrix_values">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
488 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
489
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
490 <xml name="input_graphic_output_settings">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
491 <conditional name="output" >
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
492 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
493 <option value="no" selected="true">no</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
494 <option value="yes">yes</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
495 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
496 <when value="no" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
497 <when value="yes">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
498 <yield />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
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."/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
501 </when>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
502 </conditional>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
503 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
504
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
505 <xml name="input_image_file_format">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
506 <param name="outFileFormat" type="select" label="Image file format">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
507 <option value="png" selected="true">png</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
508 <option value="pdf">pdf</option>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
509 <option value="svg">svg</option>
79d10df2108e 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>
79d10df2108e 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>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
512 </param>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
513 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
514
79d10df2108e 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">
79d10df2108e 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">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
517 <change_format>
79d10df2108e 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" />
79d10df2108e 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" />
79d10df2108e 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" />
79d10df2108e 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" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
522 </change_format>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
523 </data>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
524 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
525
79d10df2108e 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">
79d10df2108e 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">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
528 <filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
529 ((
79d10df2108e 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
79d10df2108e 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
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
532 ))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
533 </filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
534 </data>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
535 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
536
79d10df2108e 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">
79d10df2108e 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 ${on_string}: averages per matrix column">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
539 <filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
540 ((
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
541 output['showOutputSettings'] == 'yes' and
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
542 output['saveData'] is True
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
543 ))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
544 </filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
545 </data>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
547 <filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
548 ((
79d10df2108e 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
79d10df2108e 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
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
551 ))
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
552 </filter>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
553 </data>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
554 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
555
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
558 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
561 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
564 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
567 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
570 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
573 </xml>
79d10df2108e 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">
79d10df2108e 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"/>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
576 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
577
79d10df2108e 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">
79d10df2108e 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"
79d10df2108e 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." />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
581 </xml>
79d10df2108e 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">
79d10df2108e 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" />
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
584 </xml>
79d10df2108e planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d
iuc
parents:
diff changeset
585 </macros>