Mercurial > repos > bgruening > hicexplorer_hicplotviewpoint

annotate macros.xml.orig @ 2:bb82a2982d3d draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:41:30 -0500
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bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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1 <macros>
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2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
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3 <<<<<<< HEAD
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4 <token name="@WRAPPER_VERSION@">2.0</token>
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5
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6 <token name="@USE_RANGE@">
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7 #if $use_range.select_use_range == "yes_use_range":
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8 --range $range_min:$range_max
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9 #end if
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10 </token>
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11
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12 =======
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13 <token name="@WRAPPER_VERSION@">2.1alpha1</token>
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14 >>>>>>> joachimwolff-master
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15 <xml name="requirements">
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16 <requirements>
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17 <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
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18 <yield />
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19 </requirements>
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20 <version_command>@BINARY@ --version</version_command>
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21 </xml>
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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 -->
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32 </xml>
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33 <xml name="use_range">
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34 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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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>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
85 <option value="BuPu">BuPu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
86 <option value="GnBu">GnBu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
87 <option value="OrRd">OrRd</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
88 <option value="PiYG">PiYG</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
89 <option value="PRGn">PRGn</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
90 <option value="PuOr">PuOr</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
91 <option value="PuRd">PuRd</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
92 <option value="PuBu">PuBu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
93 <option value="RdBu">RdBu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
94 <option value="RdGy">RdGy</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
95 <option value="RdPu">RdPu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
96 <option value="YlGn">YlGn</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
97 <option value="PuBuGn">PuBuGn</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
98 <option value="RdYlGn">RdYlGn</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
99 <option value="YlGnBu">YlGnBu</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
100 <option value="YlOrBr">YlOrBr</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
101 <option value="YlOrRd">YlOrRd</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
102 <option value="gist_gray">gist_gray</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
103 <option value="gist_stern">gist_stern</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
104 <option value="gist_earth">gist_earth</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
105 <option value="gist_yarg">gist_yarg</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
106 <option value="gist_ncar">gist_ncar</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
107 <option value="gist_rainbow">gist_rainbow</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
108 <option value="gist_heat">gist_heat</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
109 <option value="gnuplot">gnuplot</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
110 <option value="gnuplot2">gnuplot2</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
111 <option value="CMRmap">CMRmap</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
112 <option value="bwr">bwr</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
113 <option value="hsv">hsv</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
114 <option value="brg">brg</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
115 <option value="jet">jet</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
116 <option value="afmhot">afmhot</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
117 <option value="Accent_r">Accent reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
118 <option value="Spectral_r">Spectral reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
119 <option value="Set1_r">Set1 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
120 <option value="Set2_r">Set2 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
121 <option value="Set3_r">Set3 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
122 <option value="Dark2_r">Dark2 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
123 <option value="Reds_r">Reds reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
124 <option value="Oranges_r">Oranges reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
125 <option value="Greens_r">Greens reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
126 <option value="Blues_r">Blues reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
127 <option value="Greys_r">Greys reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
128 <option value="Purples_r">Purples reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
129 <option value="Paired_r">Paired reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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130 <option value="Pastel1_r">Pastel1 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
131 <option value="Pastel2_r">Pastel2 reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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132 <option value="spring_r">spring reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
133 <option value="summer_r">summer reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
134 <option value="autumn_r">autumn reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
135 <option value="winter_r">winter reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
136 <option value="hot_r">hot reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
137 <option value="coolwarm_r">coolwarm reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
138 <option value="cool_r">cool reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
139 <option value="seismic_r">seismic reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
140 <option value="terrain_r">terrain reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
141 <option value="ocean_r">ocean reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
142 <option value="rainbow_r">rainbow reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
bgruening
parents:
diff changeset
143 <option value="bone_r">bone reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
144 <option value="flag_r">flag reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
145 <option value="prism_r">prism reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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146 <option value="cubehelix_r">cubehelix reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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147 <option value="binary_r">binary reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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148 <option value="pink_r">pink reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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149 <option value="gray_r">gray reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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150 <option value="copper_r">copper reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
diff changeset
151 <option value="BrBG_r">BrBG reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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152 <option value="BuGn_r">BuGn reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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153 <option value="BuPu_r">BuPu reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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154 <option value="GnBu_r">GnBu reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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155 <option value="OrRd_r">OrRd reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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156 <option value="PiYG_r">PiYG reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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157 <option value="PRGn_r">PRGn reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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158 <option value="PuOr_r">PuOr reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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159 <option value="PuRd_r">PuRd reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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160 <option value="PuBu_r">PuBu reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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parents:
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161 <option value="RdBu_r">RdBu reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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162 <option value="RdGy_r">RdGy reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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163 <option value="RdPu_r">RdPu reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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164 <option value="YlGn_r">YlGn reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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165 <option value="PuBuGn_r">PuBuGn reversed</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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166 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
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167 <option value="RdYlGn_r">RdYlGn reversed</option>
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168 <option value="YlGnBu_r">YlGnBu reversed</option>
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169 <option value="YlOrBr_r">YlOrBr reversed</option>
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170 <option value="YlOrRd_r">YlOrRd reversed</option>
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171 <option value="gist_gray_r">gist_gray reversed</option>
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172 <option value="gist_stern_r">gist_stern reversed</option>
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173 <option value="gist_earth_r">gist_earth reversed</option>
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174 <option value="gist_yarg_r">gist_yarg reversed</option>
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175 <option value="gist_ncar_r">gist_ncar reversed</option>
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176 <option value="gist_rainbow_r">gist_rainbow reversed</option>
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177 <option value="gist_heat_r">gist_heat reversed</option>
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178 <option value="gnuplot_r">gnuplot reversed</option>
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179 <option value="gnuplot2_r">gnuplot2 reversed</option>
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180 <option value="CMRmap_r">CMRmap reversed</option>
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181 <option value="bwr_r">bwr reversed</option>
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182 <option value="hsv_r">hsv reversed</option>
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183 <option value="brg_r">brg reversed</option>
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184 <option value="jet_r">jet reversed</option>
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185 <option value="afmhot_r">afmhot reversed</option>
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186 </param>
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187 </xml>
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188
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189
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190 <xml name="multiple_input_matrices">
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191 <repeat name="input_files" title="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
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349 <xml name="multiple_input_bams">
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350 <repeat name="input_files" title="BAM files" min="2">
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351 <param name="bamfile" type="data" format="bam"
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352 label="Bam file"
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353 help="The BAM file must be sorted."/>
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354 <param name="label" type="text" size="30" optional="true" value=""
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355 label="Label"
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356 help="Label to use in the output. If not given the dataset name will be used instead."/>
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357 </repeat>
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358 </xml>
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359
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360 <xml name="multiple_input_bigwigs">
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361 <repeat name="input_files" title="BigWig files" min="2">
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362 <param name="bigwigfile" type="data" format="bigwig"
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363 label="Bigwig file"
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364 help="The Bigwig file must be sorted."/>
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365 <param name="label" type="text" size="30" optional="true" value=""
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366 label="Label"
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367 help="Label to use in the output. If not given the dataset name will be used instead."/>
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368 </repeat>
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369 </xml>
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370
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371 <xml name="plotTitle">
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372 <param name="plotTitle" type="text" value="" size="30" optional="True"
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373 label="Title of the plot"
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374 help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
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375 </xml>
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376
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377 <token name="@multiple_input_bams@">
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378 #import tempfile
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379 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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380 #set files=[]
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381 #set labels=[]
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382 #for $i in $input_files:
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383 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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384 #set $temp_input_path = $temp_input_handle.name
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385 #silent $temp_input_handle.close()
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386 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
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387 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
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388 #silent $files.append('%s.bam' % $temp_input_path)
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389
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390 ##set $files += [str($i.bamfile)]
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391 #if str($i.label.value) != "":
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392 #set $labels += ["\"%s\"" % ($i.label.value)]
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393 #else
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394 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
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395 #end if
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396 #end for
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397 </token>
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398
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399 <token name="@multiple_input_bigwigs@">
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400 #import tempfile
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401 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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402 #set files=[]
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403 #set labels=[]
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404 #for $i in $input_files:
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405 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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406 #set $temp_input_path = $temp_input_handle.name
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407 #silent $temp_input_handle.close()
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408 #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
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409 #silent $files.append('%s.bw' % $temp_input_path)
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410
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411 ##set $files += [str($i.bigwigfile)]
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412 #if str($i.label.value) != "":
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413 #set $labels += ["\"%s\"" % ($i.label.value)]
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414 #else
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415 #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
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416 #end if
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417 #end for
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418 </token>
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419
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420 <xml name="reference_genome_source">
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421 <conditional name="source">
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422 <param name="ref_source" type="select" label="Reference genome">
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423 <option value="cached">locally cached</option>
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424 <option value="history">in your history</option>
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425 </param>
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426 <when value="cached">
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427 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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428 <options from_data_table="deepTools_seqs">
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429 <filter type="sort_by" column="1" />
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430 <validator type="no_options" message="No indexes are available." />
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431 </options>
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432 </param>
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433 </when>
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434 <when value="history">
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435 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
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436 </when>
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437 </conditional>
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438 </xml>
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439
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440 <token name="@reference_genome_source@">
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441 #if $source.ref_source=="history":
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442 --genome $source.input1
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443 #else:
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444 --genome "${source.input1_2bit.fields.path}"
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445 #end if
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446 </token>
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447
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448 <xml name="effectiveGenomeSize">
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449 <conditional name="effectiveGenomeSize">
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450 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
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451 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
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452 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
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453 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
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454 <option value="93260000">ce10 (93260000)</option>
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455 <option value="121400000">dm3 (121400000)</option>
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456 <option value="2451960000" selected="true">hg19 (2451960000)</option>
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457 <option value="2150570000">mm9 (2150570000)</option>
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458 <option value="specific">user specified</option>
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459 </param>
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460 <when value="specific">
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461 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
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462 </when>
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463 <when value="2150570000" />
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464 <when value="2451960000" />
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465 <when value="121400000" />
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466 <when value="93260000" />
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467 </conditional>
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468 </xml>
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469
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470 <xml name="image_file_format">
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471 <param name="outFileFormat" type="select" label="Image file format">
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472 <option value="png" selected="true">png</option>
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473 <option value="pdf">pdf</option>
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474 <option value="svg">svg</option>
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475 <option value="eps">eps</option>
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476 <option value="emf">emf</option>
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477 </param>
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478 </xml>
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479
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480 <xml name="missingDataAsZero">
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481 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
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482 label ="Treat missing data as zero"
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483 help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
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484 </xml>
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485
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486 <xml name="input_save_matrix_values">
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487 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
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488 </xml>
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489
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490 <xml name="input_graphic_output_settings">
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491 <conditional name="output" >
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492 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
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493 <option value="no" selected="true">no</option>
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494 <option value="yes">yes</option>
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495 </param>
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496 <when value="no" />
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497 <when value="yes">
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498 <yield />
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499 <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
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500 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
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501 </when>
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502 </conditional>
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503 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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504
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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505 <xml name="input_image_file_format">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
506 <param name="outFileFormat" type="select" label="Image file format">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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507 <option value="png" selected="true">png</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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508 <option value="pdf">pdf</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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509 <option value="svg">svg</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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510 <option value="eps">eps</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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511 <option value="emf">emf</option>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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512 </param>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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513 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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514
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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515 <xml name="output_image_file_format">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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516 <data format="png" name="outFileName" label="${tool.name} image">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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517 <change_format>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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518 <when input="output.outFileFormat" value="pdf" format="pdf" />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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519 <when input="output.outFileFormat" value="svg" format="svg" />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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520 <when input="output.outFileFormat" value="eps" format="eps" />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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521 <when input="output.outFileFormat" value="emf" format="emf" />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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522 </change_format>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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523 </data>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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524 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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525
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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526 <xml name="output_save_matrix_values">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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527 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
528 <filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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529 ((
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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530 output['showOutputSettings'] == 'yes' and
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
531 output['saveMatrix'] is True
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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532 ))
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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533 </filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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534 </data>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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535 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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536
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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537 <xml name="output_graphic_outputs">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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538 <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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539 <filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
540 ((
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
541 output['showOutputSettings'] == 'yes' and
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
542 output['saveData'] is True
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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543 ))
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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544 </filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
545 </data>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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546 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
547 <filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
548 ((
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
549 output['showOutputSettings'] == 'yes' and
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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550 output['saveSortedRegions'] is True
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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551 ))
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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552 </filter>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
553 </data>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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554 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
555
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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556 <xml name="track_input_h5_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
557 <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
558 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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559 <xml name="track_input_bed_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
560 <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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561 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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562 <xml name="track_input_bedgraph_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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563 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
564 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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565 <xml name="track_input_bigwig_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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566 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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567 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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568 <xml name="track_input_bedgraph_matrix_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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diff changeset
569 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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570 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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571 <xml name="track_input_tabular_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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572 <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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573 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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574 <xml name="plot_title">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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575 <param name="title" type="text" optional="true" label="Plot title"/>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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576 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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577
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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578 <xml name="spacer_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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579 <param name="spacer_width" type="float" value="" optional="True"
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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580 label="Include spacer at the end of the track." help="Width of the spacer." />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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581 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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582 <xml name="fontsize_macro">
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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583 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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584 </xml>
bb82a2982d3d planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
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585 </macros>